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Zhang B, Zhang Y, Zhang X, Qu J, Ruan C, Liao J, Alvarez PJJ, Yu P. Enhanced Phytopathogen Biofilm Control in the Soybean Phyllosphere by the Phoresy of Bacteriophages Hitchhiking on Biocontrol Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025. [PMID: 40315344 DOI: 10.1021/acs.est.4c09851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2025]
Abstract
Phage-based biocontrol has shown notable advantages in protecting plants against pathogenic bacteria in agricultural settings compared to chemical-based bactericides. However, the efficiency and scope of phage biocontrol of pathogenic bacteria are limited by the intrinsic properties of phages. Here, we investigated pathogen biofilm eradication in the phyllosphere using the phoresy system of hitchhiking phages onto carrier biocontrol bacteria. The phoresy system efficiently removed the pathogen biofilm in the soybean phyllosphere, reducing the total biomass by 58% and phytopathogens by 82% compared to the untreated control. Biofilm eradication tests demonstrated a significant combined beneficial effect (Bliss independence model, CI < 1) as phages improved carrier bacteria colonization by 1.2-fold and carrier bacteria facilitated phage infection by 1.4-fold. Transcriptomic analysis showed that phoresy significantly enhanced motility (e.g., fliC and pilD genes) and energy metabolism (e.g., pgm and pgk genes) of carrier bacteria and suppressed the defense system (e.g., MSH3 and FLS2 genes) and energy metabolism (e.g., petB and petC genes) of pathogens. Metabolomics analysis revealed that the phoresy system stimulated the secretion of beneficial metabolites (e.g., flavonoid and tropane alkaloid) that could enhance stress response and phyllosphere protection in soybeans. Overall, the phoresy of phages hitchhiking on biocontrol bacteria offers a novel and effective strategy for phyllosphere microbiome manipulation and bacterial disease control.
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Affiliation(s)
- Bo Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ying Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xu Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Jianhua Qu
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Chujin Ruan
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf 8600, Switzerland
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering and Rice WaTER Institute, Rice University, Houston, Texas 77005, United States
| | - Pingfeng Yu
- State Key Laboratory of Soil Pollution Control and Safety, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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2
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Zhang T, Chen L, Zhu H, Wong G. Mammalian piRNA target prediction using a hierarchical attention model. BMC Bioinformatics 2025; 26:50. [PMID: 39934678 PMCID: PMC11817350 DOI: 10.1186/s12859-025-06068-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 01/29/2025] [Indexed: 02/13/2025] Open
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important roles in regulating mRNA transcript levels. Despite their significant role in regulating cellular RNA levels, the piRNA targeting rules are not well defined, especially in mammals, which poses obstacles to the elucidation of piRNA function. RESULTS Given the complexity and current limitation in understanding the mammalian piRNA targeting rules, we designed a deep learning model by selecting appropriate deep learning sub-networks based on the targeting patterns of piRNA inferred from previous experiments. Additionally, to alleviate the problem of insufficient data, a transfer learning approach was employed. Our model achieves a good discriminatory power (Accuracy: 98.5%) in predicting an independent test dataset. Finally, this model was utilized to predict the targets of all mouse and human piRNAs available in the piRNA database. CONCLUSIONS In this research, we developed a deep learning framework that significantly advances the prediction of piRNA targets, overcoming the limitations posed by insufficient data and current incomplete targeting rules. The piRNA target prediction network and results can be downloaded from https://github.com/SofiaTianjiaoZhang/piRNATarget .
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Affiliation(s)
- Tianjiao Zhang
- School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, 529020, China.
| | - Liang Chen
- Department of Computer Science and Technology, College of Mathematics and Computer, Shantou University, Shantou, 515821, China
| | - Haibin Zhu
- Department of Statistics and Data Science, School of Economics, Jinan University, Guangzhou, 510632, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
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3
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Poole RJ, Flames N, Cochella L. Neurogenesis in Caenorhabditis elegans. Genetics 2024; 228:iyae116. [PMID: 39167071 PMCID: PMC11457946 DOI: 10.1093/genetics/iyae116] [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: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/23/2024] Open
Abstract
Animals rely on their nervous systems to process sensory inputs, integrate these with internal signals, and produce behavioral outputs. This is enabled by the highly specialized morphologies and functions of neurons. Neuronal cells share multiple structural and physiological features, but they also come in a large diversity of types or classes that give the nervous system its broad range of functions and plasticity. This diversity, first recognized over a century ago, spurred classification efforts based on morphology, function, and molecular criteria. Caenorhabditis elegans, with its precisely mapped nervous system at the anatomical level, an extensive molecular description of most of its neurons, and its genetic amenability, has been a prime model for understanding how neurons develop and diversify at a mechanistic level. Here, we review the gene regulatory mechanisms driving neurogenesis and the diversification of neuron classes and subclasses in C. elegans. We discuss our current understanding of the specification of neuronal progenitors and their differentiation in terms of the transcription factors involved and ensuing changes in gene expression and chromatin landscape. The central theme that has emerged is that the identity of a neuron is defined by modules of gene batteries that are under control of parallel yet interconnected regulatory mechanisms. We focus on how, to achieve these terminal identities, cells integrate information along their developmental lineages. Moreover, we discuss how neurons are diversified postembryonically in a time-, genetic sex-, and activity-dependent manner. Finally, we discuss how the understanding of neuronal development can provide insights into the evolution of neuronal diversity.
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Affiliation(s)
- Richard J Poole
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia 46012, Spain
| | - Luisa Cochella
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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4
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Yang H, Lee D, Kim H, Cook DE, Paik YK, Andersen EC, Lee J. Glial expression of a steroidogenic enzyme underlies natural variation in hitchhiking behavior. Proc Natl Acad Sci U S A 2024; 121:e2320796121. [PMID: 38959036 PMCID: PMC11252821 DOI: 10.1073/pnas.2320796121] [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: 11/27/2023] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
Phoresy is an interspecies interaction that facilitates spatial dispersal by attaching to a more mobile species. Hitchhiking species have evolved specific traits for physical contact and successful phoresy, but the regulatory mechanisms involved in such traits and their evolution are largely unexplored. The nematode Caenorhabditis elegans displays a hitchhiking behavior known as nictation during its stress-induced developmental stage. Dauer-specific nictation behavior has an important role in natural C. elegans populations, which experience boom-and-bust population dynamics. In this study, we investigated the nictation behavior of 137 wild C. elegans strains sampled throughout the world. We identified species-wide natural variation in nictation and performed a genome-wide association mapping. We show that the variants in the promoter of nta-1, encoding a putative steroidogenic enzyme, underlie differences in nictation. This difference is due to the changes in nta-1 expression in glial cells, which implies that glial steroid metabolism regulates phoretic behavior. Population genetic analysis and geographic distribution patterns suggest that balancing selection maintained two nta-1 haplotypes that existed in ancestral C. elegans populations. Our findings contribute to further understanding of the molecular mechanism of species interaction and the maintenance of genetic diversity within natural populations.
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Affiliation(s)
- Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul08826, Republic of Korea
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Department of Biological Sciences, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Heekyeong Kim
- Yonsei Proteome Research Center, Yonsei University, Seoul03722, Republic of Korea
| | - Daniel E. Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Seoul03722, Republic of Korea
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul08826, Republic of Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul08826, Republic of Korea
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5
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Crombie TA, McKeown R, Moya ND, Evans K, Widmayer S, LaGrassa V, Roman N, Tursunova O, Zhang G, Gibson S, Buchanan C, Roberto N, Vieira R, Tanny R, Andersen E. CaeNDR, the Caenorhabditis Natural Diversity Resource. Nucleic Acids Res 2024; 52:D850-D858. [PMID: 37855690 PMCID: PMC10767927 DOI: 10.1093/nar/gkad887] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/30/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability of genomes and the expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used to identify and measure the effects of natural genetic variants on traits using quantitative genetics. Since 2016, the C. elegans Natural Diversity Resource (CeNDR) has facilitated many of these studies by providing an archive of wild strains, genome-wide sequence and variant data for each strain, and a genome-wide association (GWA) mapping portal for the C. elegans community. Here, we present an updated platform, the Caenorhabditis Natural Diversity Resource (CaeNDR), that enables quantitative genetics and genomics studies across the three Caenorhabditis species: C. elegans, C. briggsae and C. tropicalis. The CaeNDR platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CaeNDR provides new interactive tools to explore natural variation and enable GWA mappings. All CaeNDR data and tools are accessible through a freely available web portal located at caendr.org.
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Affiliation(s)
- Timothy A Crombie
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ryan McKeown
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Nicolas D Moya
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Cell, Molecular, Developmental biology, and Biophysics Graduate Program, ohns Hopkins University, Baltimore, MD, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Samuel J Widmayer
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Vincent LaGrassa
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Natalie Roman
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Orzu Tursunova
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sophia B Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Rodolfo Vieira
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Robyn E Tanny
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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6
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Williams B, Nelson M, McRobert S, Fingerut J. An easy and inexpensive method for determining the rate of individual phoretic events of nematodes. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000942. [PMID: 37811345 PMCID: PMC10556881 DOI: 10.17912/micropub.biology.000942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
Considering their limited locomotory capabilities, the cosmopolitan distribution of free-living nematodes may rely on phoretic dispersal. We describe a new, inexpensive device to investigate individual phoretic events of the nematode Caenorhabditis elegans using the pomace flies Drosophila melanogaster and Drosophila hydei over short time periods. Using our device, we replicated previous findings demonstrating that phoresis requires C. elegans to be in the dauer stage and capable of nictation. Additionally, we find that phoresis can happen on the order of seconds, and does not increase linearly with time of interaction. Using this approach can facilitate the investigation of nematode biogeography, which could provide useful insight into their, and their vector's, control.
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Affiliation(s)
- Benjamin Williams
- Biology, Saint Joseph's University, Philadelphia, Pennsylvania, United States
| | - Matthew Nelson
- Biology, Saint Joseph's University, Philadelphia, Pennsylvania, United States
| | - Scott McRobert
- Biology, Saint Joseph's University, Philadelphia, Pennsylvania, United States
| | - Jonathan Fingerut
- Biology, Saint Joseph's University, Philadelphia, Pennsylvania, United States
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7
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Zhang X, Xu XZS. Electroreception: Worms leap to insects for dispersal. Curr Biol 2023; 33:R775-R777. [PMID: 37490866 PMCID: PMC10914292 DOI: 10.1016/j.cub.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Electroreception is employed by some fishes to locate prey or predators. However, why the nematode Caenorhabditis elegans senses electric fields is unclear. A new study shows that electroreception helps these microscopic worms to attach themselves to insects for transportation.
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Affiliation(s)
- Xinxing Zhang
- Life Sciences Institute University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - X Z Shawn Xu
- Life Sciences Institute University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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8
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McClanahan PD, Golinelli L, Le TA, Temmerman L. Automated scoring of nematode nictation on a textured background. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533066. [PMID: 36993316 PMCID: PMC10055289 DOI: 10.1101/2023.03.16.533066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Entomopathogenic nematodes including Steinernema spp. play an increasingly important role as biological alternatives to chemical pesticides. The infective juveniles of these worms use nictation - a behavior in which animals stand on their tails - as a host-seeking strategy. The developmentally-equivalent dauer larvae of the free-living nematode Caenorhabditis elegans also nictate, but as a means of phoresy or "hitching a ride" to a new food source. Advanced genetic and experimental tools have been developed for C. elegans , but time-consuming manual scoring of nictation slows efforts to understand this behavior, and the textured substrates required for nictation can frustrate traditional machine vision segmentation algorithms. Here we present a Mask R-CNN-based tracker capable of segmenting C. elegans dauers and S. carpocapsae infective juveniles on a textured background suitable for nictation, and a machine learning pipeline that scores nictation behavior. We use our system to show that the nictation propensity of C. elegans from high-density liquid cultures largely mirrors their development into dauers, and to quantify nictation in S. carpocapsae infective juveniles in the presence of a potential host. This system is an improvement upon existing intensity-based tracking algorithms and human scoring which can facilitate large-scale studies of nictation and potentially other nematode behaviors.
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Affiliation(s)
- Patrick D. McClanahan
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Luca Golinelli
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Tuan Anh Le
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
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9
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Chiba T, Okumura E, Nishigami Y, Nakagaki T, Sugi T, Sato K. Caenorhabditis elegans transfers across a gap under an electric field as dispersal behavior. Curr Biol 2023:S0960-9822(23)00674-7. [PMID: 37348502 DOI: 10.1016/j.cub.2023.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/04/2023] [Accepted: 05/17/2023] [Indexed: 06/24/2023]
Abstract
Interactions between different animal species are a critical determinant of each species' evolution and range expansion. Chemical, visual, and mechanical interactions have been abundantly reported, but the importance of electric interactions is not well understood. Here, we report the discovery that the nematode Caenorhabditis elegans transfers across electric fields to achieve phoretic attachment to insects. First, we found that dauer larvae of C. elegans nictating on a substrate in a Petri dish moved directly to the lid through the air due to the electrostatic force from the lid. To more systematically investigate the transfer behavior, we constructed an assay system with well-controlled electric fields: the worms flew up regardless of whether a positive or negative electric field was applied, suggesting that an induced charge within the worm is related to this transfer. The mean take-off speed is 0.86 m/s, and the worm flies up under an electric field exceeding 200 kV/m. This worm transfer occurs even when the worms form a nictation column composed of up to 100 worms; we term this behavior "multiworm transfer." These observations led us to conclude that C. elegans can transfer and attach to the bumblebee Bombus terrestris, which was charged by rubbing with flower pollen in the lab. The charge on the bumblebee was measured with a coulomb-meter to be 806 pC, which was within the range of bumblebee charges and of the same order of flying insect charges observed in nature, suggesting that electrical interactions occur among different species.
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Affiliation(s)
- Takuya Chiba
- Graduate School of Life Science, Hokkaido University, Kita 8 Nishi 5, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Etsuko Okumura
- Yokkaichi Tech. Department, TEISO TOYOKA CO, LTD 4005-1 Shiohama, Yokkaichi, Mie 510-0863, Japan
| | - Yukinori Nishigami
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 21 Nishi 11, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Toshiyuki Nakagaki
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 21 Nishi 11, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Takuma Sugi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-0046, Japan.
| | - Katsuhiko Sato
- Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science, Hokkaido University, Kita20, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 21 Nishi 11, Kita-ku, Sapporo, Hokkaido 001-0021, Japan.
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10
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Petersen C, Krahn A, Leippe M. The nematode Caenorhabditis elegans and diverse potential invertebrate vectors predominantly interact opportunistically. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1069056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Some small animals migrate with the help of other, more mobile animals (phoresy) to leave short-lived and resource-poor habitats. The nematode Caenorhabditis elegans lives in ephemeral habitats such as compost, but has also been found associated with various potential invertebrate vectors. Little research has been done to determine if C. elegans is directly attracted to these invertebrates. To determine whether C. elegans is attracted to compounds and volatile odorants of invertebrates, we conducted chemotaxis experiments with the isopods Porcellio scaber, Oniscus asellus, and Armadillidium sp. and with Lithobius sp. myriapods, Drosophila melanogaster fruit flies, and Arion sp. slugs as representatives of natural vectors. Because phoresy is an important escape strategy in nature, especially for dauer larvae of C. elegans, we examined the attraction of the natural C. elegans isolate MY2079 in addition to the laboratory-adapted strain N2 at the dauer and L4 stage. We found that DMSO washing solution of Lithobius sp. and the odor of live D. melanogaster attracted C. elegans N2 L4 larvae. Surprisingly, the natural isolate MY2079 was not attracted to any invertebrate during either the dauer or L4 life stages and both C. elegans strains were repelled by various compounds from O. asellus, P. scaber, Armadillidium sp., Lithobius sp., and Arion sp. feces. We hypothesize that this is due to defense chemicals released by the invertebrates. Although compounds from Lithobius sp. and D. melanogaster odorants were mildly attractive, the lack of attraction to most invertebrates suggests a predominantly opportunistic association between C. elegans and invertebrate vectors.
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11
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Cockx B, Van Bael S, Boelen R, Vandewyer E, Yang H, Le TA, Dalzell JJ, Beets I, Ludwig C, Lee J, Temmerman L. Mass Spectrometry-Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes. Mol Cell Proteomics 2023; 22:100479. [PMID: 36481452 PMCID: PMC9881375 DOI: 10.1016/j.mcpro.2022.100479] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/27/2022] [Accepted: 11/20/2022] [Indexed: 12/12/2022] Open
Abstract
Neuropeptides regulate animal physiology and behavior, making them widely studied targets of functional genetics research. While the field often relies on differential -omics approaches to build hypotheses, no such method exists for neuropeptidomics. It would nonetheless be valuable for studying behaviors suspected to be regulated by neuropeptides, especially when little information is otherwise available. This includes nictation, a phoretic strategy of Caenorhabditis elegans dauers that parallels host-finding strategies of infective juveniles of many pathogenic nematodes. We here developed a targeted peptidomics method for the model organism C. elegans and show that 161 quantified neuropeptides are more abundant in its dauer stage compared with L3 juveniles. Many of these have orthologs in the commercially relevant pathogenic nematode Steinernema carpocapsae, in whose infective juveniles, we identified 126 neuropeptides in total. Through further behavioral genetics experiments, we identify flp-7 and flp-11 as novel regulators of nictation. Our work advances knowledge on the genetics of nictation behavior and adds comparative neuropeptidomics as a tool to functional genetics workflows.
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Affiliation(s)
- Bram Cockx
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Sven Van Bael
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rose Boelen
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Elke Vandewyer
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Tuan Anh Le
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Johnathan J Dalzell
- School of Biological Sciences, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Isabel Beets
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Liesbet Temmerman
- Animal Physiology & Neurobiology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium.
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12
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Hammerschmith EW, Woodruff GC, Moser KA, Johnson E, Phillips PC. Opposing directions of stage-specific body shape change in a close relative of C. elegans. BMC ZOOL 2022; 7:38. [PMID: 37170380 PMCID: PMC10127021 DOI: 10.1186/s40850-022-00131-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 05/04/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
Body size is a fundamental organismal trait. However, as body size and ecological contexts change across developmental time, evolutionary divergence may cause unexpected patterns of body size diversity among developmental stages. This may be particularly evident in polyphenic developmental stages specialized for dispersal. The dauer larva is such a stage in nematodes, and Caenorhabditis species disperse by traveling on invertebrate carriers. Here, we describe the morphology of a stress-resistant, dauer-like larval stage of the nematode Caenorhabditis inopinata, whose adults can grow to be nearly twice as long as its close relative, the model organism C. elegans.
Results
We find that a dauer-like, stress-resistant larval stage in two isolates of C. inopinata is on average 13% shorter and 30% wider than the dauer larvae of C. elegans, despite its much longer adult stage. Additionally, many C. inopinata dauer-like larvae were ensheathed, a possible novelty in this lineage reminiscent of the infective juveniles of parasitic nematodes. Variation in dauer-like larva formation frequency among twenty-four wild isolates of C. inopinata was also observed, although frequencies were low across all isolates (< 2%), with many isolates unable to produce dauer-like larvae under conventional laboratory conditions.
Conclusion
Most Caenorhabditis species thrive on rotting plants and disperse on snails, slugs, or isopods (among others) whereas C. inopinata is ecologically divergent and thrives in fresh Ficus septica figs and disperses on their pollinating wasps. While there is some unknown factor of the fig environment that promotes elongated body size in C. inopinata adults, the small size or unique life history of its fig wasp carrier may be driving the divergent morphology of its stress-resistant larval stages. Further characterization of the behavior, development, and morphology of this stage will refine connections to homologous developmental stages in other species and determine whether ecological divergence across multiple developmental stages can promote unexpected and opposing changes in body size dimensions within a single species.
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13
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Widmayer SJ, Evans KS, Zdraljevic S, Andersen EC. Evaluating the power and limitations of genome-wide association studies in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2022; 12:jkac114. [PMID: 35536194 PMCID: PMC9258552 DOI: 10.1093/g3journal/jkac114] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
Quantitative genetics in Caenorhabditis elegans seeks to identify naturally segregating genetic variants that underlie complex traits. Genome-wide association studies scan the genome for individual genetic variants that are significantly correlated with phenotypic variation in a population, or quantitative trait loci. Genome-wide association studies are a popular choice for quantitative genetic analyses because the quantitative trait loci that are discovered segregate in natural populations. Despite numerous successful mapping experiments, the empirical performance of genome-wide association study has not, to date, been formally evaluated in C. elegans. We developed an open-source genome-wide association study pipeline called NemaScan and used a simulation-based approach to provide benchmarks of mapping performance in collections of wild C. elegans strains. Simulated trait heritability and complexity determined the spectrum of quantitative trait loci detected by genome-wide association studies. Power to detect smaller-effect quantitative trait loci increased with the number of strains sampled from the C. elegans Natural Diversity Resource. Population structure was a major driver of variation in mapping performance, with populations shaped by recent selection exhibiting significantly lower false discovery rates than populations composed of more divergent strains. We also recapitulated previous genome-wide association studies of experimentally validated quantitative trait variants. Our simulation-based evaluation of performance provides the community with critical context to pursue quantitative genetic studies using the C. elegans Natural Diversity Resource to elucidate the genetic basis of complex traits in C. elegans natural populations.
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Affiliation(s)
- Samuel J Widmayer
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Kathryn S Evans
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Stefan Zdraljevic
- Department of Biological Chemistry, University of California—Los Angeles, Los Angeles, CA 90095, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
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14
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Ahn S, Yang H, Son S, Lee HS, Park D, Yim H, Choi HJ, Swoboda P, Lee J. The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization. Cell Rep 2022; 39:110661. [PMID: 35417689 DOI: 10.1016/j.celrep.2022.110661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
Cilia are important for the interaction with environments and the proper function of tissues. While the basic structure of cilia is well conserved, ciliated cells have various functions. To understand the distinctive identities of ciliated cells, the identification of cell-specific proteins and its regulation is essential. Here, we report the mechanism that confers a specific identity on IL2 neurons in Caenorhabditis elegans, neurons important for the dauer larva-specific nictation behavior. We show that DAF-19M, an isoform of the sole C. elegans RFX transcription factor DAF-19, heads a regulatory subroutine, regulating target genes through an X-box motif variant under the control of terminal selector proteins UNC-86 and CFI-1 in IL2 neurons. Considering the conservation of DAF-19M module in IL2 neurons for nictation and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature "recognizing the environment."
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Affiliation(s)
- Soungyub Ahn
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Sangwon Son
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyun Sik Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dongjun Park
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
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15
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Dysregulation of Human Somatic piRNA Expression in Parkinson's Disease Subtypes and Stages. Int J Mol Sci 2022; 23:ijms23052469. [PMID: 35269612 PMCID: PMC8910154 DOI: 10.3390/ijms23052469] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Piwi interacting RNAs (piRNAs) are small non-coding single-stranded RNA species 20–31 nucleotides in size generated from distinct loci. In germline tissues, piRNAs are amplified via a “ping-pong cycle” to produce secondary piRNAs, which act in transposon silencing. In contrast, the role of somatic-derived piRNAs remains obscure. Here, we investigated the identity and distribution of piRNAs in human somatic tissues to determine their function and potential role in Parkinson’s disease (PD). Human datasets were curated from the Gene Expression Omnibus (GEO) database and a workflow was developed to identify piRNAs, which revealed 902 somatic piRNAs of which 527 were expressed in the brain. These were mainly derived from chromosomes 1, 11, and 19 compared to the germline tissues, which were from 15 and 19. Approximately 20% of somatic piRNAs mapped to transposon 3′ untranslated regions (UTRs), but a large proportion were sensed to the transcript in contrast to germline piRNAs. Gene set enrichment analysis suggested that somatic piRNAs function in neurodegenerative disease. piRNAs undergo dysregulation in different PD subtypes (PD and Parkinson’s disease dementia (PDD)) and stages (premotor and motor). piR-has-92056, piR-hsa-150797, piR-hsa-347751, piR-hsa-1909905, piR-hsa-2476630, and piR-hsa-2834636 from blood small extracellular vesicles were identified as novel biomarkers for PD diagnosis using a sparse partial least square discriminant analysis (sPLS-DA) (accuracy: 92%, AUC = 0.89). This study highlights a role for piRNAs in PD and provides tools for novel biomarker development.
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16
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Ow MC, Hall SE. piRNAs and endo-siRNAs: Small molecules with large roles in the nervous system. Neurochem Int 2021; 148:105086. [PMID: 34082061 PMCID: PMC8286337 DOI: 10.1016/j.neuint.2021.105086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/23/2021] [Accepted: 05/26/2021] [Indexed: 01/02/2023]
Abstract
Since their discovery, small non-coding RNAs have emerged as powerhouses in the regulation of numerous cellular processes. In addition to guarding the integrity of the reproductive system, small non-coding RNAs play critical roles in the maintenance of the soma. Accumulating evidence indicates that small non-coding RNAs perform vital functions in the animal nervous system such as restricting the activity of deleterious transposable elements, regulating nerve regeneration, and mediating learning and memory. In this review, we provide an overview of the current understanding of the contribution of two major classes of small non-coding RNAs, piRNAs and endo-siRNAs, to the nervous system development and function, and present highlights on how the dysregulation of small non-coding RNA pathways can assist in understanding the neuropathology of human neurological disorders.
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Affiliation(s)
- Maria C Ow
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| | - Sarah E Hall
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
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17
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Evans KS, van Wijk MH, McGrath PT, Andersen EC, Sterken MG. From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation. Trends Genet 2021; 37:933-947. [PMID: 34229867 DOI: 10.1016/j.tig.2021.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 11/15/2022]
Abstract
Although many studies have examined quantitative trait variation across many species, only a small number of genes and thereby molecular mechanisms have been discovered. Without these data, we can only speculate about evolutionary processes that underlie trait variation. Here, we review how quantitative and molecular genetics in the nematode Caenorhabditis elegans led to the discovery and validation of 37 quantitative trait genes over the past 15 years. Using these data, we can start to make inferences about evolution from these quantitative trait genes, including the roles that coding versus noncoding variation, gene family expansion, common versus rare variants, pleiotropy, and epistasis play in trait variation across this species.
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Affiliation(s)
- Kathryn S Evans
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Marijke H van Wijk
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
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18
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Guisnet A, Maitra M, Pradhan S, Hendricks M. A three-dimensional habitat for C. elegans environmental enrichment. PLoS One 2021; 16:e0245139. [PMID: 33428657 PMCID: PMC7799825 DOI: 10.1371/journal.pone.0245139] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/22/2020] [Indexed: 11/19/2022] Open
Abstract
As we learn more about the importance of gene-environment interactions and the effects of environmental enrichment, it becomes evident that minimalistic laboratory conditions can affect gene expression patterns and behaviors of model organisms. In the laboratory, Caenorhabditis elegans is generally cultured on two-dimensional, homogeneous agar plates abundantly covered with axenic bacteria culture as a food source. However, in the wild, this nematode thrives in rotting fruits and plant stems feeding on bacteria and small eukaryotes. This contrast in habitat complexity suggests that studying C. elegans in enriched laboratory conditions can deepen our understanding of its fundamental traits and behaviors. Here, we developed a protocol to create three-dimensional habitable scaffolds for trans-generational culture of C. elegans in the laboratory. Using decellularization and sterilization of fruit tissue, we created an axenic environment that can be navigated throughout and where the microbial environment can be strictly controlled. C. elegans were maintained over generations on this habitat, and showed a clear behavioral bias for the enriched environment. As an initial assessment of behavioral variations, we found that dauer populations in scaffolds exhibit high-frequency, complex nictation behavior including group towering and jumping behavior.
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Affiliation(s)
- Aurélie Guisnet
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | - Malosree Maitra
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | - Sreeparna Pradhan
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
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19
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Evans KS, Zdraljevic S, Stevens L, Collins K, Tanny RE, Andersen EC. Natural variation in the sequestosome-related gene, sqst-5, underlies zinc homeostasis in Caenorhabditis elegans. PLoS Genet 2020; 16:e1008986. [PMID: 33175833 PMCID: PMC7682890 DOI: 10.1371/journal.pgen.1008986] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/23/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc is an essential trace element that acts as a co-factor for many enzymes and transcription factors required for cellular growth and development. Altering intracellular zinc levels can produce dramatic effects ranging from cell proliferation to cell death. To avoid such fates, cells have evolved mechanisms to handle both an excess and a deficiency of zinc. Zinc homeostasis is largely maintained via zinc transporters, permeable channels, and other zinc-binding proteins. Variation in these proteins might affect their ability to interact with zinc, leading to either increased sensitivity or resistance to natural zinc fluctuations in the environment. We can leverage the power of the roundworm nematode Caenorhabditis elegans as a tractable metazoan model for quantitative genetics to identify genes that could underlie variation in responses to zinc. We found that the laboratory-adapted strain (N2) is resistant and a natural isolate from Hawaii (CB4856) is sensitive to micromolar amounts of exogenous zinc supplementation. Using a panel of recombinant inbred lines, we identified two large-effect quantitative trait loci (QTL) on the left arm of chromosome III and the center of chromosome V that are associated with zinc responses. We validated and refined both QTL using near-isogenic lines (NILs) and identified a naturally occurring deletion in sqst-5, a sequestosome-related gene, that is associated with resistance to high exogenous zinc. We found that this deletion is relatively common across strains within the species and that variation in sqst-5 is associated with zinc resistance. Our results offer a possible mechanism for how organisms can respond to naturally high levels of zinc in the environment and how zinc homeostasis varies among individuals.
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Affiliation(s)
- Kathryn S. Evans
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Stefan Zdraljevic
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Lewis Stevens
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Kimberly Collins
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Robyn E. Tanny
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Erik C. Andersen
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
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20
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Abstract
Nictation is a behaviour in which a nematode stands on its tail and waves its head in three dimensions. This activity promotes dispersal of dauer larvae by allowing them to attach to other organisms and travel on them to a new niche. In this review, we describe our understanding of nictation, including its diversity in nematode species, how it is induced by environmental factors, and neurogenetic factors that regulate nictation. We also highlight the known cellular and signalling factors that affect nictation, for example, IL2 neurons, insulin/IGF-1 signalling, TGF-β signalling, FLP neuropeptides and piRNAs. Elucidation of the mechanism of nictation will contribute to increased understanding of the conserved dispersal strategies in animals.
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Affiliation(s)
- Heeseung Yang
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Bo Yun Lee
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, South Korea
| | - Hyunsoo Yim
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul, South Korea
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21
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The Gene scb-1 Underlies Variation in Caenorhabditis elegans Chemotherapeutic Responses. G3-GENES GENOMES GENETICS 2020; 10:2353-2364. [PMID: 32385045 PMCID: PMC7341127 DOI: 10.1534/g3.120.401310] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pleiotropy, the concept that a single gene controls multiple distinct traits, is prevalent in most organisms and has broad implications for medicine and agriculture. The identification of the molecular mechanisms underlying pleiotropy has the power to reveal previously unknown biological connections between seemingly unrelated traits. Additionally, the discovery of pleiotropic genes increases our understanding of both genetic and phenotypic complexity by characterizing novel gene functions. Quantitative trait locus (QTL) mapping has been used to identify several pleiotropic regions in many organisms. However, gene knockout studies are needed to eliminate the possibility of tightly linked, non-pleiotropic loci. Here, we use a panel of 296 recombinant inbred advanced intercross lines of Caenorhabditis elegans and a high-throughput fitness assay to identify a single large-effect QTL on the center of chromosome V associated with variation in responses to eight chemotherapeutics. We validate this QTL with near-isogenic lines and pair genome-wide gene expression data with drug response traits to perform mediation analysis, leading to the identification of a pleiotropic candidate gene, scb-1, for some of the eight chemotherapeutics. Using deletion strains created by genome editing, we show that scb-1, which was previously implicated in response to bleomycin, also underlies responses to other double-strand DNA break-inducing chemotherapeutics. This finding provides new evidence for the role of scb-1 in the nematode drug response and highlights the power of mediation analysis to identify causal genes.
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22
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The nematode Caenorhabditis elegans and the terrestrial isopod Porcellio scaber likely interact opportunistically. PLoS One 2020; 15:e0235000. [PMID: 32589676 PMCID: PMC7319334 DOI: 10.1371/journal.pone.0235000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/06/2020] [Indexed: 11/19/2022] Open
Abstract
Phoresy is a behavior in which an organism, the phoront, travels from one location to another by 'hitching a ride' on the body of a host as it disperses. Some phoronts are generalists, taking advantage of any available host. Others are specialists and travel only when specific hosts are located using chemical cues to identify and move (chemotax) toward the preferred host. Free-living nematodes, like Caenorhabditis elegans, are often found in natural environments that contain terrestrial isopods and other invertebrates. Additionally, the C. elegans wild strain PB306 was isolated associated with the isopod Porcellio scaber. However, it is currently unclear if C. elegans is a phoront of terrestrial isopods, and if so, whether it is a specialist, generalist, or developmental stage-specific combination of both strategies. Because the relevant chemical stimuli might be secreted compounds or volatile odorants, we used different types of chemotaxis assays across diverse extractions of compounds or odorants to test whether C. elegans is attracted to P. scaber. We show that two different strains-the wild isolate PB306 and the laboratory-adapted strain N2 -are not attracted to P. scaber during either the dauer or adult life stages. Our results indicate that C. elegans was not attracted to chemical compounds or volatile odorants from P. scaber, providing valuable empirical evidence to suggest that any associations between these two species are likely opportunistic rather than specific phoresy.
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23
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Wu WS, Brown JS, Chen TT, Chu YH, Huang WC, Tu S, Lee HC. piRTarBase: a database of piRNA targeting sites and their roles in gene regulation. Nucleic Acids Res 2020; 47:D181-D187. [PMID: 30357353 PMCID: PMC6323935 DOI: 10.1093/nar/gky956] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small noncoding RNAs that guard animal genomes against mutation by silencing transposons. In addition, recent studies have reported that piRNAs silence various endogenous genes. Tens of thousands of distinct piRNAs made in animals do not pair well to transposons and currently the functions and targets of piRNAs are largely unexplored. piRTarBase provides a user-friendly interface to access both predicted and experimentally identified piRNA targeting sites in Caenorhabditis elegans. The user can input genes of interest and retrieve a list of piRNA targeting sites on the input genes. Alternatively, the user can input a piRNA and retrieve a list of its mRNA targets. Additionally, piRTarBase integrates published mRNA and small RNA sequencing data, which will help users identify biologically relevant targeting events. Importantly, our analyses suggest that the piRNA sites found by both predictive and experimental approaches are more likely to exhibit silencing effects on their targets than each method alone. Taken together, piRTarBase offers an integrative platform that will help users to identify functional piRNA target sites by evaluating various information. piRTarBase is freely available for academic use at http://cosbi6.ee.ncku.edu.tw/piRTarBase/.
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Affiliation(s)
- Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Jordan S Brown
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Tsung-Te Chen
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Han Chu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Che Huang
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Shikui Tu
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Heng-Chi Lee
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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24
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Snoek BL, Sterken MG, Hartanto M, van Zuilichem AJ, Kammenga JE, de Ridder D, Nijveen H. WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans. Database (Oxford) 2020; 2020:baz149. [PMID: 31960906 PMCID: PMC6971878 DOI: 10.1093/database/baz149] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 12/19/2022]
Abstract
Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and understanding of the underlying molecular components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here, we present WormQTL2, a database and platform for comparative investigations and meta-analyses of published (e)QTL data sets in the model nematode worm C. elegans. WormQTL2 integrates six eQTL studies spanning 11 conditions as well as over 1000 traits from 32 studies and allows experimental results to be compared, reused and extended upon to guide further experiments and conduct systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs that could be linked to variation in other traits, detect gene-by-environment interactions by comparing eQTLs under different conditions, or find correlations between QTL profiles of classical traits and gene expression. WormQTL2 makes data on natural variation in C. elegans and the identified QTLs interactively accessible, allowing studies beyond the original publications. Database URL: www.bioinformatics.nl/WormQTL2/.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Margi Hartanto
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Albert-Jan van Zuilichem
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
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25
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Kim KW. PIWI Proteins and piRNAs in the Nervous System. Mol Cells 2019; 42:828-835. [PMID: 31838836 PMCID: PMC6939654 DOI: 10.14348/molcells.2019.0241] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/29/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
PIWI Argonaute proteins and Piwi-interacting RNAs (piRNAs) are expressed in all animal species and play a critical role in cellular defense by inhibiting the activation of transposable elements in the germline. Recently, new evidence suggests that PIWI proteins and piRNAs also play important roles in various somatic tissues, including neurons. This review summarizes the neuronal functions of the PIWI-piRNA pathway in multiple animal species, including their involvement in axon regeneration, behavior, memory formation, and transgenerational epigenetic inheritance of adaptive memory. This review also discusses the consequences of dysregulation of neuronal PIWI-piRNA pathways in certain neurological disorders, including neurodevelopmental and neurodegenerative diseases. A full understanding of neuronal PIWI-piRNA pathways will ultimately provide novel insights into small RNA biology and could potentially provide precise targets for therapeutic applications.
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Affiliation(s)
- Kyung Won Kim
- Convergence Program of Material Science for Medicine and Pharmaceutics, Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252,
Korea
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26
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Suvorov A, Naumov V, Shtratnikova V, Logacheva M, Shershebnev A, Wu H, Gerasimov E, Zheludkevich A, Pilsner JR, Sergeyev O. Rat liver epigenome programing by perinatal exposure to 2,2',4'4'-tetrabromodiphenyl ether. Epigenomics 2019; 12:235-249. [PMID: 31833787 DOI: 10.2217/epi-2019-0315] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Perinatal exposures to polybrominated diphenyl ethers permanently reprogram liver metabolism and induce a nonalcoholic fatty liver disease-like phenotype and insulin resistance in rodents. Aim: To test if these changes are associated with altered liver epigenome. Materials & methods: Expression of small RNA and changes in DNA methylation in livers of adult rats were analyzed following perinatal exposure to 2,2',4,4'-tetrabromodiphenyl ether, the polybrominated diphenyl ether congener most prevalent in human tissues. Results: We identified 33 differentially methylated DNA regions and 15 differentially expressed miRNAs. These changes were enriched for terms related to lipid and carbohydrate metabolism, insulin signaling, Type-2 diabetes and nonalcoholic fatty liver disease. Conclusion: Changes in the liver epigenome are a likely candidate mechanism of long-term maintenance of an aberrant metabolic phenotype.
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Affiliation(s)
- Alexander Suvorov
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA.,A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia
| | - Vladimir Naumov
- Kulakov National Medical Research Center of Obstetrics, Gynecology & Perinatology, Ministry of Health of the Russian Federation, Oparina 4, 117997, Moscow, Russia
| | - Victoria Shtratnikova
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia.,Center for Data-Intensive Biomedicine & Biotechnology, Skolkovo Institute of Science & Technology, 143028, Moscow, Russia
| | - Maria Logacheva
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia.,Center for Data-Intensive Biomedicine & Biotechnology, Skolkovo Institute of Science & Technology, 143028, Moscow, Russia
| | - Alex Shershebnev
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA.,Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, 722 W 168th St, New York, NY 10032, USA
| | - Evgeny Gerasimov
- E.I. Martsinovsky Institute of Medical Parasitology & Tropical Medicine, I.M. Sechenov First Moscow State Medical University, 20 Malaya Pirogovskaya, 119435, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | | | - Jonathan R Pilsner
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts 686 North Pleasant Street Amherst, MA 01003, USA
| | - Oleg Sergeyev
- A.N. Belozersky Research Institute of Physico-Chemical Biology, Moscow State University, Leninskye Gory, House 1, Building 40, 119992, Moscow, Russia.,Chapaevsk Medical Association, 3a Meditsinskaya St., Samara region, 446100, Chapaevsk, Russia
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27
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Warnock ND, Cox D, McCoy C, Morris R, Dalzell JJ. Transcriptional variation and divergence of host-finding behaviour in Steinernema carpocapsae infective juveniles. BMC Genomics 2019; 20:884. [PMID: 31752671 PMCID: PMC6868747 DOI: 10.1186/s12864-019-6179-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 10/10/2019] [Indexed: 11/15/2022] Open
Abstract
Background Steinernema carpocapsae is an entomopathogenic nematode that employs nictation and jumping behaviours to find potential insect hosts. Here we aimed to investigate the transcriptional basis of variant host-finding behaviours in the infective juvenile (IJ) stage of three S. carpocapsae strains (ALL, Breton and UK1), with a focus on neuronal genes known to influence behaviour in other nematode species. Identifying gene expression changes that correlate with variant host-finding behaviours will further our understanding of nematode biology. Results RNA-seq analysis revealed that whilst up to 28% of the S. carpocapsae transcriptome was differentially expressed (P < 0.0001) between strains, remarkably few of the most highly differentially expressed genes (> 2 log2 fold change, P < 0.0001) were from neuronal gene families. S. carpocapsae Breton displays increased chemotaxis toward the laboratory host Galleria mellonella, relative to the other strains. This correlates with the up-regulation of four srsx chemosensory GPCR genes, and a sodium transporter gene, asic-2, relative to both ALL and UK1 strains. The UK1 strain exhibits a decreased nictation phenotype relative to ALL and Breton strains, which correlates with co-ordinate up-regulation of neuropeptide like protein 36 (nlp-36), and down-regulation of an srt family GPCR gene, and a distinct asic-2-like sodium channel paralogue. To further investigate the link between transcriptional regulation and behavioural variation, we sequenced microRNAs across IJs of each strain. We have identified 283 high confidence microRNA genes, yielding 321 predicted mature microRNAs in S. carpocapsae, and find that up to 36% of microRNAs are differentially expressed (P < 0.0001) between strains. Many of the most highly differentially expressed microRNAs (> 2 log2 fold, P < 0.0001) are predicted to regulate a variety of neuronal genes that may contribute to variant host-finding behaviours. We have also found evidence for differential gene isoform usage between strains, which alters predicted microRNA interactions, and could contribute to the diversification of behaviour. Conclusions These data provide insight to the transcriptional basis of behavioural variation in S. carpocapsae, supporting efforts to understand the molecular basis of complex behaviours in nematodes.
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Affiliation(s)
- Neil D Warnock
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Deborah Cox
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Ciaran McCoy
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Robert Morris
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
| | - Johnathan J Dalzell
- School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland.
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Selection and gene flow shape niche-associated variation in pheromone response. Nat Ecol Evol 2019; 3:1455-1463. [PMID: 31548647 PMCID: PMC6764921 DOI: 10.1038/s41559-019-0982-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/14/2019] [Indexed: 11/18/2022]
Abstract
From quorum sensing in bacteria to pheromone signaling in social insects, chemical communication mediates interactions among individuals in a local population. In Caenorhabditis elegans, ascaroside pheromones can dictate local population density, in which high levels of pheromones inhibit the reproductive maturation of individuals. Little is known about how natural genetic diversity affects the pheromone responses of individuals from diverse habitats. Here, we show that a niche-associated variation in pheromone receptor genes contributes to natural differences in pheromone responses. We identified putative loss-of-function deletions that impair duplicated pheromone receptor genes (srg-36 and srg-37), which were shown previously to be lost in population-dense laboratory cultures. A common natural deletion in srg-37 arose recently from a single ancestral population that spread throughout the world and underlies reduced pheromone sensitivity across the global C. elegans population. We found that many local populations harbor individuals with wild-type or a deletion allele of srg-37, suggesting that balancing selection has maintained the recent variation in this pheromone receptor gene. The two srg-37 genotypes are associated with niche diversity underlying boom-and-bust population dynamics. We hypothesize that human activities likely contributed to the gene flow and balancing selection of srg-37 variation through facilitating migration of species and providing favorable niche for recently arose srg-37 deletion.
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29
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Ascaroside Pheromones: Chemical Biology and Pleiotropic Neuronal Functions. Int J Mol Sci 2019; 20:ijms20163898. [PMID: 31405082 PMCID: PMC6719183 DOI: 10.3390/ijms20163898] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/1970] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
Pheromones are neuronal signals that stimulate conspecific individuals to react to environmental stressors or stimuli. Research on the ascaroside (ascr) pheromones in Caenorhabditis elegans and other nematodes has made great progress since ascr#1 was first isolated and biochemically defined in 2005. In this review, we highlight the current research on the structural diversity, biosynthesis, and pleiotropic neuronal functions of ascr pheromones and their implications in animal physiology. Experimental evidence suggests that ascr biosynthesis starts with conjugation of ascarylose to very long-chain fatty acids that are then processed via peroxisomal β-oxidation to yield diverse ascr pheromones. We also discuss the concentration and stage-dependent pleiotropic neuronal functions of ascr pheromones. These functions include dauer induction, lifespan extension, repulsion, aggregation, mating, foraging and detoxification, among others. These roles are carried out in coordination with three G protein-coupled receptors that function as putative pheromone receptors: SRBC-64/66, SRG-36/37, and DAF-37/38. Pheromone sensing is transmitted in sensory neurons via DAF-16-regulated glutamatergic neurotransmitters. Neuronal peroxisomal fatty acid β-oxidation has important cell-autonomous functions in the regulation of neuroendocrine signaling, including neuroprotection. In the future, translation of our knowledge of nematode ascr pheromones to higher animals might be beneficial, as ascr#1 has some anti-inflammatory effects in mice. To this end, we propose the establishment of pheromics (pheromone omics) as a new subset of integrated disciplinary research area within chemical ecology for system-wide investigation of animal pheromones.
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30
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Brady SC, Zdraljevic S, Bisaga KW, Tanny RE, Cook DE, Lee D, Wang Y, Andersen EC. A Novel Gene Underlies Bleomycin-Response Variation in Caenorhabditis elegans. Genetics 2019; 212:1453-1468. [PMID: 31171655 PMCID: PMC6707474 DOI: 10.1534/genetics.119.302286] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022] Open
Abstract
Bleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organism Caenorhabditis elegans to identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain (N2) and a wild strain (CB4856). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines, and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene (scb-1) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function of scb-1 between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance.
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Affiliation(s)
- Shannon C Brady
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208
| | - Stefan Zdraljevic
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208
| | - Karol W Bisaga
- Weinberg College of Arts and Sciences, Northwestern University, Evanston, Illinois 60208
| | - Robyn E Tanny
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | | | - Daehan Lee
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Ye Wang
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Erik C Andersen
- Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611
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31
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Kim C, Kim J, Kim S, Cook DE, Evans KS, Andersen EC, Lee J. Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans. Genome Res 2019; 29:1023-1035. [PMID: 31123081 PMCID: PMC6581047 DOI: 10.1101/gr.246082.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/22/2019] [Indexed: 12/05/2022]
Abstract
Long-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes are generated and tolerated within a species, we sequenced a C. elegans strain, CB4856, which is one of the most genetically divergent strains compared to the N2 reference strain. For this comparison, we used the Pacific Biosciences (PacBio) RSII platform (80×, N50 read length 11.8 kb) and generated de novo genome assembly to the level of pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb). We identified structural variations that affected as many as 2694 genes, most of which are at chromosome arms. Subtelomeric regions contained the most extensive genomic rearrangements, which even created new subtelomeres in some cases. The subtelomere structure of Chromosome VR implies that ancestral telomere damage was repaired by alternative lengthening of telomeres even in the presence of a functional telomerase gene and that a new subtelomere was formed by break-induced replication. Our study demonstrates that substantial genomic changes including structural variations and new subtelomeres can be tolerated within a species, and that these changes may accumulate genetic diversity within a species.
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Affiliation(s)
- Chuna Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
| | - Sunghyun Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea 08826
- Department of Biological Sciences, Seoul National University, Seoul, Korea 08826
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea 08826
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32
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Snoek BL, Volkers RJM, Nijveen H, Petersen C, Dirksen P, Sterken MG, Nakad R, Riksen JAG, Rosenstiel P, Stastna JJ, Braeckman BP, Harvey SC, Schulenburg H, Kammenga JE. A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits. BMC Biol 2019; 17:24. [PMID: 30866929 PMCID: PMC6417139 DOI: 10.1186/s12915-019-0642-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/26/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale. RESULTS To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. CONCLUSION Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands. .,Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Carola Petersen
- Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Philipp Dirksen
- Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Rania Nakad
- Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, 24098, Kiel, Germany
| | - Jana J Stastna
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
| | - Bart P Braeckman
- Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Simon C Harvey
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
| | - Hinrich Schulenburg
- Zoological Institute, University of Kiel, 24098, Kiel, Germany. .,Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
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Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses. Genetics 2018; 210:1509-1525. [PMID: 30341085 PMCID: PMC6283156 DOI: 10.1534/genetics.118.301311] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/16/2018] [Indexed: 01/25/2023] Open
Abstract
Phenotypic complexity is caused by the contributions of environmental factors and multiple genetic loci, interacting or acting independently. Studies of yeast and Arabidopsis often find that the majority of natural variation across phenotypes is attributable to independent additive quantitative trait loci (QTL). Detected loci in these organisms explain most of the estimated heritable variation. By contrast, many heritable components underlying phenotypic variation in metazoan models remain undetected. Before the relative impacts of additive and interactive variance components on metazoan phenotypic variation can be dissected, high replication and precise phenotypic measurements are required to obtain sufficient statistical power to detect loci contributing to this missing heritability. Here, we used a panel of 296 recombinant inbred advanced intercross lines of Caenorhabditis elegans and a high-throughput fitness assay to detect loci underlying responses to 16 different toxins, including heavy metals, chemotherapeutic drugs, pesticides, and neuropharmaceuticals. Using linkage mapping, we identified 82 QTL that underlie variation in responses to these toxins, and predicted the relative contributions of additive loci and genetic interactions across various growth parameters. Additionally, we identified three genomic regions that impact responses to multiple classes of toxins. These QTL hotspots could represent common factors impacting toxin responses. We went further to generate near-isogenic lines and chromosome substitution strains, and then experimentally validated these QTL hotspots, implicating additive and interactive loci that underlie toxin-response variation.
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Pristionchus nematodes occur frequently in diverse rotting vegetal substrates and are not exclusively necromenic, while Panagrellus redivivoides is found specifically in rotting fruits. PLoS One 2018; 13:e0200851. [PMID: 30074986 PMCID: PMC6075748 DOI: 10.1371/journal.pone.0200851] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/05/2018] [Indexed: 01/31/2023] Open
Abstract
The lifestyle and feeding habits of nematodes are highly diverse. Several species of Pristionchus (Nematoda: Diplogastridae), including Pristionchus pacificus, have been reported to be necromenic, i.e. to associate with beetles in their dauer diapause stage and wait until the death of their host to resume development and feed on microbes in the decomposing beetle corpse. We review the literature and suggest that the association of Pristionchus to beetles may be phoretic and not necessarily necromenic. The view that Pristionchus nematodes have a necromenic lifestyle is based on studies that have sought Pristionchus only by sampling live beetles. By surveying for nematode genera in different types of rotting vegetal matter, we found Pristionchus spp. at a similar high frequency as Caenorhabditis, often in large numbers and in feeding stages. Thus, these Pristionchus species may feed in decomposing vegetal matter. In addition, we report that one species of Panagrellus (Nematoda: Panagrolaimidae), Panagrellus redivivoides, is found in rotting fruits but not in rotting stems, with a likely association with Drosophila fruitflies. Based on our sampling and the observed distribution of feeding and dauer stages, we propose a life cycle for Pristionchus nematodes and Panagrellus redivivoides that is similar to that of C. elegans, whereby they feed on the microbial blooms on decomposing vegetal matter and are transported between food patches by coleopterans for Pristionchus spp., fruitflies for Panagrellus redivivoides and isopods and terrestrial molluscs for C. elegans.
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35
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DiBlasi E, Johnson KP, Stringham SA, Hansen AN, Beach AB, Clayton DH, Bush SE. Phoretic dispersal influences parasite population genetic structure. Mol Ecol 2018; 27:2770-2779. [PMID: 29752753 DOI: 10.1111/mec.14719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/15/2018] [Accepted: 04/18/2018] [Indexed: 01/01/2023]
Abstract
Dispersal is a fundamental component of the life history of most species. Dispersal influences fitness, population dynamics, gene flow, genetic drift and population genetic structure. Even small differences in dispersal can alter ecological interactions and trigger an evolutionary cascade. Linking such ecological processes with evolutionary patterns is difficult, but can be carried out in the proper comparative context. Here, we investigate how differences in phoretic dispersal influence the population genetic structure of two different parasites of the same host species. We focus on two species of host-specific feather lice (Phthiraptera: Ischnocera) that co-occur on feral rock pigeons (Columba livia). Although these lice are ecologically very similar, "wing lice" (Columbicola columbae) disperse phoretically by "hitchhiking" on pigeon flies (Diptera: Hippoboscidae), while "body lice" (Campanulotes compar) do not. Differences in the phoretic dispersal of these species are thought to underlie observed differences in host specificity, as well as the degree of host-parasite cospeciation. These ecological and macroevolutionary patterns suggest that body lice should exhibit more genetic differentiation than wing lice. We tested this prediction among lice on individual birds and among lice on birds from three pigeon flocks. We found higher levels of genetic differentiation in body lice compared to wing lice at two spatial scales. Our results indicate that differences in phoretic dispersal can explain microevolutionary differences in population genetic structure and are consistent with macroevolutionary differences in the degree of host-parasite cospeciation.
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Affiliation(s)
- Emily DiBlasi
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois
| | | | - Angela N Hansen
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Andrew B Beach
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Dale H Clayton
- Department of Biology, University of Utah, Salt Lake City, Utah
| | - Sarah E Bush
- Department of Biology, University of Utah, Salt Lake City, Utah
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36
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Richaud A, Zhang G, Lee D, Lee J, Félix MA. The Local Coexistence Pattern of Selfing Genotypes in Caenorhabditis elegans Natural Metapopulations. Genetics 2018; 208:807-821. [PMID: 29242287 PMCID: PMC5788539 DOI: 10.1534/genetics.117.300564] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/09/2017] [Indexed: 02/08/2023] Open
Abstract
To study the interplay of rare outcrossing and metapopulation structure, we focus on the nematode Caenorhabditis elegans Its remarkably low outcrossing rate is at the extreme end of the spectrum for facultative selfing organisms. At the demographic level, C. elegans natural populations undergo boom and bust dynamics on ephemeral resources, with the dauer diapause larva acting as the dispersal form. Here we investigate the small-scale genetic structure of C. elegans populations in two localities over several years, using 2b restriction-associated DNA sequencing of nearly 1000 individuals. We find a remarkably small number of genome-wide haplotypes, almost exclusively in the homozygous state, confirming the low effective outcrossing rate. Most strikingly, the major haplotypes in a locality remain intact and do not effectively recombine over several years. From the spatial pattern of diversity, we estimate that each subpopulation or deme is seeded by a mean of 3-10 immigrating individuals. Populations are thus formed by clones that compete at two levels, within a subpopulation and at the metapopulation level. We test for the presence of local phenotypic variation in pathogen resistance and dauer larva nictation, which could possibly explain the maintenance of different genotypes by heterogeneous selection in different local environments or lifecycles. This study is the first to address the local spatiotemporal genetic structure of C. elegans on feeding substrates. We conclude that these animals coexist as competing homozygous clones at the smallest population scale as well as in the metapopulation.
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Affiliation(s)
- Aurélien Richaud
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Gaotian Zhang
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Daehan Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Marie-Anne Félix
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
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37
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GIBSON AMANDAK, MORRAN LEVIT. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites. J Nematol 2018. [DOI: 10.21307/jofnem-2017-083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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38
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Gibson AK, Morran LT. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites. J Nematol 2017; 49:357-372. [PMID: 29353923 PMCID: PMC5770282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 06/07/2023] Open
Abstract
Many of the outstanding questions in disease ecology and evolution call for combining observation of natural host-parasite populations with experimental dissection of interactions in the field and the laboratory. The "rewilding" of model systems holds great promise for this endeavor. Here, we highlight the potential for development of the nematode Caenorhabditis elegans and its close relatives as a model for the study of disease ecology and evolution. This powerful laboratory model was disassociated from its natural habitat in the 1960s. Today, studies are uncovering that lost natural history, with several natural parasites described since 2008. Studies of these natural Caenorhabditis-parasite interactions can reap the benefits of the vast array of experimental and genetic tools developed for this laboratory model. In this review, we introduce the natural parasites of C. elegans characterized thus far and discuss resources available to study them, including experimental (co)evolution, cryopreservation, behavioral assays, and genomic tools. Throughout, we present avenues of research that are interesting and feasible to address with caenorhabditid nematodes and their natural parasites, ranging from the maintenance of outcrossing to the community dynamics of host-associated microbes. In combining natural relevance with the experimental power of a laboratory supermodel, these fledgling host-parasite systems can take on fundamental questions in evolutionary ecology of disease.
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Affiliation(s)
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, GA 30322
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Kim J, Lee D, Lee J. A quantitative trait locus for nictation behavior on chromosome V. MICROPUBLICATION BIOLOGY 2017; 2017:10.17912/W23D39. [PMID: 32550361 PMCID: PMC7255881 DOI: 10.17912/w23d39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jun Kim
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Daehan Lee
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea,
Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Junho Lee
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea,
Correspondence to: Junho Lee ()
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