1
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Slowinski SP, Gresham JD, Cui ER, Haspel K, Lively CM, Morran LT. Outcrossing in Caenorhabditis elegans increases in response to food limitation. Ecol Evol 2024; 14:e11166. [PMID: 38516572 PMCID: PMC10954511 DOI: 10.1002/ece3.11166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 02/05/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
Theory predicts that organisms should diversify their offspring when faced with a stressful environment. This prediction has received empirical support across diverse groups of organisms and stressors. For example, when encountered by Caenorhabditis elegans during early development, food limitation (a common environmental stressor) induces the nematodes to arrest in a developmental stage called dauer and to increase their propensity to outcross when they are subsequently provided with food and enabled to develop to maturity. Here we tested whether food limitation first encountered during late development/early adulthood can also induce increased outcrossing propensity in C. elegans. Previously well-fed C. elegans increased their propensity to outcross when challenged with food limitation during the final larval stage of development and into early adulthood, relative to continuously well-fed (control) nematodes. Our results thus support previous research demonstrating that the stress of food limitation can induce increased outcrossing propensity in C. elegans. Furthermore, our results expand on previous work by showing that food limitation can still increase outcrossing propensity even when it is not encountered until late development, and this can occur independently of the developmental and gene expression changes associated with dauer.
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Affiliation(s)
- Samuel P. Slowinski
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
- Department BiologyUniversity of MarylandCollege ParkMarylandUSA
| | | | - Eric R. Cui
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
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2
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Cowen MH, Reddy KC, Chalasani SH, Hart MP. Conserved autism-associated genes tune social feeding behavior in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570116. [PMID: 38106124 PMCID: PMC10723370 DOI: 10.1101/2023.12.05.570116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Animal foraging is an essential and evolutionarily conserved behavior that occurs in social and solitary contexts, but the underlying molecular pathways are not well defined. We discover that conserved autism-associated genes (NRXN1(nrx-1), NLGN3(nlg-1), GRIA1,2,3(glr-1), GRIA2(glr-2), and GLRA2,GABRA3(avr-15)) regulate aggregate feeding in C. elegans, a simple social behavior. NRX-1 functions in chemosensory neurons (ADL and ASH) independently of its postsynaptic partner NLG-1 to regulate social feeding. Glutamate from these neurons is also crucial for aggregate feeding, acting independently of NRX-1 and NLG-1. Compared to solitary counterparts, social animals show faster presynaptic release and more presynaptic release sites in ASH neurons, with only the latter requiring nrx-1. Disruption of these distinct signaling components additively converts behavior from social to solitary. Aggregation induced by circuit activation is also dependent on nrx-1. Collectively, we find that aggregate feeding is tuned by conserved autism-associated genes through complementary synaptic mechanisms, revealing molecular principles driving social feeding.
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Affiliation(s)
- Mara H. Cowen
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
- Autism Spectrum Program of Excellence, Perelman School of Medicine, Philadelphia, PA
| | - Kirthi C. Reddy
- Molecular Neurobiology Laboratory, Salk Institute, La Jolla, CA
| | | | - Michael P. Hart
- Department of Genetics, University of Pennsylvania, Philadelphia, PA
- Autism Spectrum Program of Excellence, Perelman School of Medicine, Philadelphia, PA
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3
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Long L, Xu W, Valencia F, Paaby AB, McGrath PT. A toxin-antidote selfish element increases fitness of its host. eLife 2023; 12:e81640. [PMID: 37874324 PMCID: PMC10629817 DOI: 10.7554/elife.81640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/23/2023] [Indexed: 10/25/2023] Open
Abstract
Selfish genetic elements can promote their transmission at the expense of individual survival, creating conflict between the element and the rest of the genome. Recently, a large number of toxin-antidote (TA) post-segregation distorters have been identified in non-obligate outcrossing nematodes. Their origin and the evolutionary forces that keep them at intermediate population frequencies are poorly understood. Here, we study a TA element in Caenorhabditis elegans called zeel-1;peel-1. Two major haplotypes of this locus, with and without the selfish element, segregate in C. elegans. We evaluate the fitness consequences of the zeel-1;peel-1 element outside of its role in gene drive in non-outcrossing animals and demonstrate that loss of the toxin peel-1 decreased fitness of hermaphrodites and resulted in reductions in fecundity and body size. These findings suggest a biological role for peel-1 beyond toxin lethality. This work demonstrates that a TA element can provide a fitness benefit to its hosts either during their initial evolution or by being co-opted by the animals following their selfish spread. These findings guide our understanding on how TA elements can remain in a population where gene drive is minimized, helping resolve the mystery of prevalent TA elements in selfing animals.
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Affiliation(s)
- Lijiang Long
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Wen Xu
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
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4
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Yeon J, Porwal C, McGrath PT, Sengupta P. Identification of a spontaneously arising variant affecting thermotaxis behavior in a recombinant inbred Caenorhabditis elegans line. G3 (BETHESDA, MD.) 2023; 13:jkad186. [PMID: 37572357 PMCID: PMC10542565 DOI: 10.1093/g3journal/jkad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 06/26/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
Analyses of the contributions of genetic variants in wild strains to phenotypic differences have led to a more complete description of the pathways underlying cellular functions. Causal loci are typically identified via interbreeding of strains with distinct phenotypes in order to establish recombinant inbred lines (RILs). Since the generation of RILs requires growth for multiple generations, their genomes may contain not only different combinations of parental alleles but also genetic changes that arose de novo during the establishment of these lines. Here, we report that in the course of generating RILs between Caenorhabditis elegans strains that exhibit distinct thermotaxis behavioral phenotypes, we identified spontaneously arising variants in the ttx-1 locus. ttx-1 encodes the terminal selector factor for the AFD thermosensory neurons, and loss-of-function mutations in ttx-1 abolish thermotaxis behaviors. The identified genetic changes in ttx-1 in the RIL are predicted to decrease ttx-1 function in part via specifically affecting a subset of AFD-expressed ttx-1 isoforms. Introduction of the relevant missense mutation in the laboratory C. elegans strain via gene editing recapitulates the thermotaxis behavioral defects of the RIL. Our results suggest that spontaneously occurring genomic changes in RILs may complicate identification of loci contributing to phenotypic variation, but that these mutations may nevertheless lead to the identification of important causal molecules and mechanisms.
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Affiliation(s)
- Jihye Yeon
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Charmi Porwal
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
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5
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Bell AD, Chou HT, Valencia F, Paaby AB. Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad112. [PMID: 37221008 PMCID: PMC10411595 DOI: 10.1093/g3journal/jkad112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023]
Abstract
Though natural systems harbor genetic and phenotypic variation, research in model organisms is often restricted to a reference strain. Focusing on a reference strain yields a great depth of knowledge but potentially at the cost of breadth of understanding. Furthermore, tools developed in the reference context may introduce bias when applied to other strains, posing challenges to defining the scope of variation within model systems. Here, we evaluate how genetic differences among 5 wild Caenorhabditis elegans strains affect gene expression and its quantification, in general and after induction of the RNA interference (RNAi) response. Across strains, 34% of genes were differentially expressed in the control condition, including 411 genes that were not expressed at all in at least 1 strain; 49 of these were unexpressed in reference strain N2. Reference genome mapping bias caused limited concern: despite hyperdiverse hotspots throughout the genome, 92% of variably expressed genes were robust to mapping issues. The transcriptional response to RNAi was highly strain- and target-gene-specific and did not correlate with RNAi efficiency, as the 2 RNAi-insensitive strains showed more differentially expressed genes following RNAi treatment than the RNAi-sensitive reference strain. We conclude that gene expression, generally and in response to RNAi, differs across C. elegans strains such that the choice of strain may meaningfully influence scientific inferences. Finally, we introduce a resource for querying gene expression variation in this dataset at https://wildworm.biosci.gatech.edu/rnai/.
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Affiliation(s)
- Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
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6
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van Wijk MH, Davies AG, Sterken MG, Mathies LD, Quamme EC, Blackwell GG, Riksen JAG, Kammenga JE, Bettinger JC. Natural allelic variation modifies acute ethanol response phenotypes in wild strains of C. elegans. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2023; 47:1505-1517. [PMID: 37356915 DOI: 10.1111/acer.15139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND Genetic variation contributes to the likelihood that an individual will develop an alcohol use disorder (AUD). Traditional laboratory studies in animal models have elucidated the molecular pharmacology of ethanol, but laboratory-derived genetic manipulations rarely model the naturally occurring genetic variation observed in wild populations. Rather, these manipulations are biased toward identifying genes of central importance in the phenotypes. Because changes in such genes can confer selective disadvantages, they are not ideal candidates for carrying AUD risk alleles in humans. We sought to exploit Caenorhabditis elegans to identify allelic variation existing in the wild that modulates ethanol response behaviors. METHODS We tested the acute ethanol responses of four strains recently isolated from the wild (JU1511, JU1926, JU1931, and JU1941) and 41 multiparental recombinant inbred lines (mpRILs) derived from them. We assessed locomotion at 10, 30, and 50 min on low and high ethanol concentrations. We performed principal component analyses (PCA) on the different phenotypes, tested for transgressive behavior, calculated heritability, and determined the correlations between behavioral responses. RESULTS We observed a range of responses to ethanol across the strains. We detected a low-concentration locomotor activation effect in some of the mpRILs not seen in the laboratory wild-type strain. PCA showed different ethanol response behaviors to be independent. We observed transgressive behavior for many of the measured phenotypes and found that multiple behaviors were uncorrelated. The average broad-sense heritability for all phenotypes was 23.2%. CONCLUSIONS Genetic variation significantly affects multiple acute ethanol response behaviors, many of which are independent of one another. This suggests that the genetic variation captured by these strains likely affects multiple biological mechanisms through which ethanol acts. Further study of these strains may allow these distinct mechanisms to be identified.
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Affiliation(s)
- Marijke H van Wijk
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Andrew G Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Elizabeth C Quamme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - GinaMari G Blackwell
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, Virginia, USA
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7
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Bell AD, Chou HT, Paaby AB. Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.533964. [PMID: 36993640 PMCID: PMC10055391 DOI: 10.1101/2023.03.24.533964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A universal feature of living systems is that natural variation in genotype underpins variation in phenotype. Yet, research in model organisms is often constrained to a single genetic background, the reference strain. Further, genomic studies that do evaluate wild strains typically rely on the reference strain genome for read alignment, leading to the possibility of biased inferences based on incomplete or inaccurate mapping; the extent of reference bias can be difficult to quantify. As an intermediary between genome and organismal traits, gene expression is well positioned to describe natural variability across genotypes generally and in the context of environmental responses, which can represent complex adaptive phenotypes. C. elegans sits at the forefront of investigation into small-RNA gene regulatory mechanisms, or RNA interference (RNAi), and wild strains exhibit natural variation in RNAi competency following environmental triggers. Here, we examine how genetic differences among five wild strains affect the C. elegans transcriptome in general and after inducing RNAi responses to two germline target genes. Approximately 34% of genes were differentially expressed across strains; 411 genes were not expressed at all in at least one strain despite robust expression in others, including 49 genes not expressed in reference strain N2. Despite the presence of hyper-diverse hotspots throughout the C. elegans genome, reference mapping bias was of limited concern: over 92% of variably expressed genes were robust to mapping issues. Overall, the transcriptional response to RNAi was strongly strain-specific and highly specific to the target gene, and the laboratory strain N2 was not representative of the other strains. Moreover, the transcriptional response to RNAi was not correlated with RNAi phenotypic penetrance; the two germline RNAi incompetent strains exhibited substantial differential gene expression following RNAi treatment, indicating an RNAi response despite failure to reduce expression of the target gene. We conclude that gene expression, both generally and in response to RNAi, differs across C. elegans strains such that choice of strain may meaningfully influence scientific conclusions. To provide a public, easily accessible resource for querying gene expression variation in this dataset, we introduce an interactive website at https://wildworm.biosci.gatech.edu/rnai/ .
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Affiliation(s)
- Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Annalise B. Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
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8
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GLB-3: A resilient, cysteine-rich, membrane-tethered globin expressed in the reproductive and nervous system of Caenorhabditis elegans. J Inorg Biochem 2023; 238:112063. [PMID: 36370505 DOI: 10.1016/j.jinorgbio.2022.112063] [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: 09/14/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022]
Abstract
The popular genetic model organism Caenorhabditis elegans (C. elegans) encodes 34 globins, whereby the few that are well-characterized show divergent properties besides the typical oxygen carrier function. Here, we present a biophysical characterization and expression analysis of C. elegans globin-3 (GLB-3). GLB-3 is predicted to exist in two isoforms and is expressed in the reproductive and nervous system. Knockout of this globin causes a 99% reduction in fertility and reduced motility. Spectroscopic analysis reveals that GLB-3 exists as a bis-histidyl-ligated low-spin form in both the ferrous and ferric heme form. A function in binding of diatomic gases is excluded on the basis of the slow CO-binding kinetics. Unlike other globins, GLB-3 is also not capable of reacting with H2O2, H2S, and nitrite. Intriguingly, not only does GLB-3 contain a high number of cysteine residues, it is also highly stable under harsh conditions (pH = 2 and high concentrations of H2O2). The resilience diminishes when the N- and C-terminal extensions are removed. Redox potentiometric measurements reveal a slightly positive redox potential (+8 ± 19 mV vs. SHE), suggesting that the heme iron may be able to oxidize cysteines. Electron paramagnetic resonance shows that formation of an intramolecular disulphide bridge, involving Cys70, affects the heme-pocket region. The results suggest an involvement of the globin in (cysteine) redox chemistry.
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9
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Wang W, Flury AG, Rodriguez AT, Garrison JL, Brem RB. A role for worm cutl-24 in background- and parent-of-origin-dependent ER stress resistance. BMC Genomics 2022; 23:842. [PMID: 36539699 PMCID: PMC9764823 DOI: 10.1186/s12864-022-09063-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Organisms in the wild can acquire disease- and stress-resistance traits that outstrip the programs endogenous to humans. Finding the molecular basis of such natural resistance characters is a key goal of evolutionary genetics. Standard statistical-genetic methods toward this end can perform poorly in organismal systems that lack high rates of meiotic recombination, like Caenorhabditis worms. RESULTS Here we discovered unique ER stress resistance in a wild Kenyan C. elegans isolate, which in inter-strain crosses was passed by hermaphrodite mothers to hybrid offspring. We developed an unbiased version of the reciprocal hemizygosity test, RH-seq, to explore the genetics of this parent-of-origin-dependent phenotype. Among top-scoring gene candidates from a partial-coverage RH-seq screen, we focused on the neuronally-expressed, cuticlin-like gene cutl-24 for validation. In gene-disruption and controlled crossing experiments, we found that cutl-24 was required in Kenyan hermaphrodite mothers for ER stress tolerance in their inter-strain hybrid offspring; cutl-24 was also a contributor to the trait in purebred backgrounds. CONCLUSIONS These data establish the Kenyan strain allele of cutl-24 as a determinant of a natural stress-resistant state, and they set a precedent for the dissection of natural trait diversity in invertebrate animals without the need for a panel of meiotic recombinants.
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Affiliation(s)
- Wenke Wang
- Buck Institute for Research on Aging, Novato, CA, United States
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, United States
| | - Anna G Flury
- Buck Institute for Research on Aging, Novato, CA, United States
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, United States
| | - Andrew T Rodriguez
- Buck Institute for Research on Aging, Novato, CA, United States
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
| | - Jennifer L Garrison
- Buck Institute for Research on Aging, Novato, CA, United States.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States.
- Department of Cellular and Molecular Pharmacology, UC San Francisco, San Francisco, CA, United States.
- Global Consortium for Reproductive Longevity & Equality, Novato, CA, United States.
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, CA, United States.
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, United States.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States.
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10
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Yoon KH, Indong RA, Lee JI. Making "Sense" of Ecology from a Genetic Perspective: Caenorhabditis elegans, Microbes and Behavior. Metabolites 2022; 12:1084. [PMID: 36355167 PMCID: PMC9697003 DOI: 10.3390/metabo12111084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 12/31/2023] Open
Abstract
Our knowledge of animal and behavior in the natural ecology is based on over a century's worth of valuable field studies. In this post-genome era, however, we recognize that genes are the underpinning of ecological interactions between two organisms. Understanding how genes contribute to animal ecology, which is essentially the intersection of two genomes, is a tremendous challenge. The bacterivorous nematode Caenorhabditis elegans, one of the most well-known genetic animal model experimental systems, experiences a complex microbial world in its natural habitat, providing us with a window into the interplay of genes and molecules that result in an animal-microbial ecology. In this review, we will discuss C. elegans natural ecology, how the worm uses its sensory system to detect the microbes and metabolites that it encounters, and then discuss some of the fascinating ecological dances, including behaviors, that have evolved between the nematode and the microbes in its environment.
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Affiliation(s)
- Kyoung-hye Yoon
- Department of Physiology, Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju 26426, Korea
| | - Rocel Amor Indong
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Wonju 26493, Korea
| | - Jin I. Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Wonju 26493, Korea
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11
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A set of hub neurons and non-local connectivity features support global brain dynamics in C. elegans. Curr Biol 2022; 32:3443-3459.e8. [PMID: 35809568 DOI: 10.1016/j.cub.2022.06.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/17/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022]
Abstract
The wiring architecture of neuronal networks is assumed to be a strong determinant of their dynamical computations. An ongoing effort in neuroscience is therefore to generate comprehensive synapse-resolution connectomes alongside brain-wide activity maps. However, the structure-function relationship, i.e., how the anatomical connectome and neuronal dynamics relate to each other on a global scale, remains unsolved. Systematically, comparing graph features in the C. elegans connectome with correlations in nervous system-wide neuronal dynamics, we found that few local connectivity motifs and mostly other non-local features such as triplet motifs and input similarities can predict functional relationships between neurons. Surprisingly, quantities such as connection strength and amount of common inputs do not improve these predictions, suggesting that the network's topology is sufficient. We demonstrate that hub neurons in the connectome are key to these relevant graph features. Consistently, inhibition of multiple hub neurons specifically disrupts brain-wide correlations. Thus, we propose that a set of hub neurons and non-local connectivity features provide an anatomical substrate for global brain dynamics.
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12
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Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife 2022; 11:68040. [PMID: 35201977 PMCID: PMC8871372 DOI: 10.7554/elife.68040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 02/07/2022] [Indexed: 12/05/2022] Open
Abstract
Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome.
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Affiliation(s)
- Giulio Valperga
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Mario de Bono
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
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13
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Andersen EC, Rockman MV. Natural genetic variation as a tool for discovery in Caenorhabditis nematodes. Genetics 2022; 220:iyab156. [PMID: 35134197 PMCID: PMC8733454 DOI: 10.1093/genetics/iyab156] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/11/2021] [Indexed: 11/12/2022] Open
Abstract
Over the last 20 years, studies of Caenorhabditis elegans natural diversity have demonstrated the power of quantitative genetic approaches to reveal the evolutionary, ecological, and genetic factors that shape traits. These studies complement the use of the laboratory-adapted strain N2 and enable additional discoveries not possible using only one genetic background. In this chapter, we describe how to perform quantitative genetic studies in Caenorhabditis, with an emphasis on C. elegans. These approaches use correlations between genotype and phenotype across populations of genetically diverse individuals to discover the genetic causes of phenotypic variation. We present methods that use linkage, near-isogenic lines, association, and bulk-segregant mapping, and we describe the advantages and disadvantages of each approach. The power of C. elegans quantitative genetic mapping is best shown in the ability to connect phenotypic differences to specific genes and variants. We will present methods to narrow genomic regions to candidate genes and then tests to identify the gene or variant involved in a quantitative trait. The same features that make C. elegans a preeminent experimental model animal contribute to its exceptional value as a tool to understand natural phenotypic variation.
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Affiliation(s)
- Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
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14
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Abstract
Studies of C. elegans behavior have been crucial in identifying genetic pathways that control nervous system development and function, as well as basic principles of neural circuit function. Modern analysis of C. elegans behavior commonly relies on video recordings of animals, followed by automated image analysis and behavior quantification. Here, we describe two methods for recording and quantifying C. elegans behavior: a single-worm tracking approach that provides high-resolution behavioral data for individual animals and a multi-worm tracking approach that allows for quantification of the behavior of many animals in parallel. These approaches should be useful to a wide range of researchers studying the nervous system and behavior of C. elegans.
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Affiliation(s)
- Navin Pokala
- Department of Biological and Chemical Sciences, Theobald Science Center, New York Institute of Technology, Old Westbury, NY, USA.
| | - Steven W Flavell
- Department of Brain & Cognitive Sciences, Picower Institute for Learning & Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
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15
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Heaton A, Milligan E, Faulconer E, Allen A, Nguyen T, Weir SM, Glaberman S. Variation in copper sensitivity between laboratory and wild strains of Caenorhabditis elegans. CHEMOSPHERE 2022; 287:131883. [PMID: 34818820 DOI: 10.1016/j.chemosphere.2021.131883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Ecological risk assessments of chemicals are frequently based on laboratory toxicity data from a small number of model species that may be reared in labs for years or decades. These populations can undergo many processes in the lab including artificial selection, founder effect, and genetic drift, and may not adequately represent their wild counterparts, potentially undermining the goal of protecting natural populations. Here we measure variation in lethality to copper chloride among strains of an emerging model species in toxicology, Caenorhabditis elegans. We tested four wild strains from Chile, Germany, Kenya, and Madeira (Portugal) against several versions of the standard laboratory N2 strain from Bristol, UK used in molecular biology. The four wild strains were more sensitive than any of the N2 strains tested with copper. We also found that the standard N2 strain cultured in the laboratory for >1 year was less sensitive than a recently cultured N2 strain as well as a cataloged ancestral version of the N2 strain. These results suggest that toxicologists should be cognizant of performing toxicity testing with long-held animal cultures, and should perhaps use multiple strains as well as renew cultures periodically in the laboratory. This study also shows that multi-strain toxicity testing with nematodes is highly achievable and useful for understanding variation in intra- and interspecific chemical sensitivity.
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Affiliation(s)
- Andrew Heaton
- Department of Biology, University of South Alabama, Mobile, AL, USA; Grand Bay National Estuarine Research Reserve, Moss Point, MS, USA
| | - Emma Milligan
- Department of Biology, University of South Alabama, Mobile, AL, USA
| | | | - Andrew Allen
- Department of Biology, University of South Alabama, Mobile, AL, USA
| | - Timothy Nguyen
- Department of Biology, University of South Alabama, Mobile, AL, USA
| | - Scott M Weir
- Department of Biology, Queens University of Charlotte, Charlotte, NC, USA
| | - Scott Glaberman
- Department of Biology, University of South Alabama, Mobile, AL, USA; Department of Environmental Science & Policy, George Mason University, Fairfax, VA, USA.
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16
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Snoek BL, Sterken MG, Nijveen H, Volkers RJM, Riksen J, Rosenstiel PC, Schulenburg H, Kammenga JE. The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population. G3 (BETHESDA, MD.) 2021; 11:jkab258. [PMID: 34568931 PMCID: PMC8496280 DOI: 10.1093/g3journal/jkab258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022]
Abstract
Studying genetic variation of gene expression provides a powerful way to unravel the molecular components underlying complex traits. Expression quantitative trait locus (eQTL) studies have been performed in several different model species, yet most of these linkage studies have been based on the genetic segregation of two parental alleles. Recently, we developed a multiparental segregating population of 200 recombinant inbred lines (mpRILs) derived from four wild isolates (JU1511, JU1926, JU1931, and JU1941) in the nematode Caenorhabditis elegans. We used RNA-seq to investigate how multiple alleles affect gene expression in these mpRILs. We found 1789 genes differentially expressed between the parental lines. Transgression, expression beyond any of the parental lines in the mpRILs, was found for 7896 genes. For expression QTL mapping almost 9000 SNPs were available. By combining these SNPs and the RNA-seq profiles of the mpRILs, we detected almost 6800 eQTLs. Most trans-eQTLs (63%) co-locate in six newly identified trans-bands. The trans-eQTLs found in previous two-parental allele eQTL experiments and this study showed some overlap (17.5-46.8%), highlighting on the one hand that a large group of genes is affected by polymorphic regulators across populations and conditions, on the other hand, it shows that the mpRIL population allows identification of novel gene expression regulatory loci. Taken together, the analysis of our mpRIL population provides a more refined insight into C. elegans complex trait genetics and eQTLs in general, as well as a starting point to further test and develop advanced statistical models for detection of multiallelic eQTLs and systems genetics studying the genotype-phenotype relationship.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Joost Riksen
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Philip C Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, 24098 Kiel, Germany
- Competence Centre for Genomic Analysis (CCGA) Kiel, University of Kiel, 24098 Kiel, Germany
| | - Hinrich Schulenburg
- Zoological Institute, University of Kiel, 24098 Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306 Ploen, Germany
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
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17
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Zhang G, Mostad JD, Andersen EC. Natural variation in fecundity is correlated with species-wide levels of divergence in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2021; 11:jkab168. [PMID: 33983439 PMCID: PMC8496234 DOI: 10.1093/g3journal/jkab168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/03/2021] [Indexed: 01/08/2023]
Abstract
Life history traits underlie the fitness of organisms and are under strong natural selection. A new mutation that positively impacts a life history trait will likely increase in frequency and become fixed in a population (e.g., a selective sweep). The identification of the beneficial alleles that underlie selective sweeps provides insights into the mechanisms that occurred during the evolution of a species. In the global population of Caenorhabditis elegans, we previously identified selective sweeps that have drastically reduced chromosomal-scale genetic diversity in the species. Here, we measured the fecundity of 121 wild C. elegans strains, including many recently isolated divergent strains from the Hawaiian islands and found that strains with larger swept genomic regions have significantly higher fecundity than strains without evidence of the recent selective sweeps. We used genome-wide association (GWA) mapping to identify three quantitative trait loci (QTL) underlying the fecundity variation. In addition, we mapped previous fecundity data from wild C. elegans strains and C. elegans recombinant inbred advanced intercross lines that were grown in various conditions and detected eight QTL using GWA and linkage mappings. These QTL show the genetic complexity of fecundity across this species. Moreover, the haplotype structure in each GWA QTL region revealed correlations with recent selective sweeps in the C. elegans population. North American and European strains had significantly higher fecundity than most strains from Hawaii, a hypothesized origin of the C. elegans species, suggesting that beneficial alleles that caused increased fecundity could underlie the selective sweeps during the worldwide expansion of C. elegans.
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Affiliation(s)
- Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Jake D Mostad
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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18
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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: 27] [Impact Index Per Article: 9.0] [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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19
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Abergel Z, Shaked M, Shukla V, Wu ZX, Gross E. The phosphatidylinositol transfer protein PITP-1 facilitates fast recovery of eating behavior after hypoxia in the nematode Caenorhabditis elegans. FASEB J 2021; 35:e21202. [PMID: 33368638 PMCID: PMC7839455 DOI: 10.1096/fj.202000704r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022]
Abstract
Among the fascinating adaptations to limiting oxygen conditions (hypoxia) is the suppression of food intake and weight loss. In humans, this phenomenon is called high-altitude anorexia and is observed in people suffering from acute mountain syndrome. The high-altitude anorexia appears to be conserved in evolution and has been seen in species across the animal kingdom. However, the mechanism underlying the recovery of eating behavior after hypoxia is still not known. Here, we show that the phosphatidylinositol transfer protein PITP-1 is essential for the fast recovery of eating behavior after hypoxia in the nematode Caenorhabditis elegans. Unlike the neuroglobin GLB-5 that accelerates the recovery of eating behavior through its function in the oxygen (O2 )-sensing neurons, PITP-1 appears to act downstream, in neurons that express the mod-1 serotonin receptor. Indeed, pitp-1 mutants display wild-type-like O2 -evoked-calcium responses in the URX O2 -sensing neuron. Intriguingly, loss-of-function of protein kinase C 1 (PKC-1) rescues pitp-1 mutants' recovery after hypoxia. Increased diacylglycerol (DAG), which activates PKC-1, attenuates the recovery of wild-type worms. Together, these data suggest that PITP-1 enables rapid recovery of eating behavior after hypoxia by limiting DAG's availability, thereby limiting PKC activity in mod-1-expressing neurons.
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Affiliation(s)
- Zohar Abergel
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maayan Shaked
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Virendra Shukla
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zheng-Xing Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biophysics and Molecular Physiology, College of Life Science and Technology, Institute of Biophysics and Biochemistry, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Einav Gross
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
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20
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Dubois C, Gupta S, Mugler A, Félix MA. Temporally regulated cell migration is sensitive to variation in body size. Development 2021; 148:dev196949. [PMID: 33593818 PMCID: PMC10683003 DOI: 10.1242/dev.196949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
Few studies have measured the robustness to perturbations of the final position of a long-range migrating cell. In the nematode Caenorhabditis elegans, the QR neuroblast migrates anteriorly, while undergoing three division rounds. We study the final position of two of its great-granddaughters, the end of migration of which was previously shown to depend on a timing mechanism. We find that the variance in their final position is similar to that of other long-range migrating neurons. As expected from the timing mechanism, the position of QR descendants depends on body size, which we varied by changing maternal age or using body size mutants. Using a mathematical model, we show that body size variation is partially compensated for. Applying environmental perturbations, we find that the variance in final position increased following starvation at hatching. The mean position is displaced upon a temperature shift. Finally, highly significant variation was found among C. elegans wild isolates. Overall, this study reveals that the final position of these neurons is quite robust to stochastic variation, shows some sensitivity to body size and to external perturbations, and varies in the species.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Clément Dubois
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
| | - Shivam Gupta
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, 75005 Paris, France
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21
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Li Q, Marcu DC, Palazzo O, Turner F, King D, Spires-Jones TL, Stefan MI, Busch KE. High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans. eLife 2020; 9:59711. [PMID: 33228848 PMCID: PMC7685709 DOI: 10.7554/elife.59711] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022] Open
Abstract
The ability to learn progressively declines with age. Neural hyperactivity has been implicated in impairing cognitive plasticity with age, but the molecular mechanisms remain elusive. Here, we show that chronic excitation of the Caenorhabditis elegans O2-sensing neurons during ageing causes a rapid decline of experience-dependent plasticity in response to environmental O2 concentration, whereas sustaining lower activity of O2-sensing neurons retains plasticity with age. We demonstrate that neural activity alters the ageing trajectory in the transcriptome of O2-sensing neurons, and our data suggest that high-activity neurons redirect resources from maintaining plasticity to sustaining continuous firing. Sustaining plasticity with age requires the K+-dependent Na+/Ca2+ (NCKX) exchanger, whereas the decline of plasticity with age in high-activity neurons acts through calmodulin and the scaffold protein Kidins220. Our findings demonstrate directly that the activity of neurons alters neuronal homeostasis to govern the age-related decline of neural plasticity and throw light on the mechanisms involved.
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Affiliation(s)
- Qiaochu Li
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel-Cosmin Marcu
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ottavia Palazzo
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Frances Turner
- Edinburgh Genomics (Genome Science), Ashworth Laboratories, The University of Edinburgh, Edinburgh, United Kingdom
| | - Declan King
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom.,United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tara L Spires-Jones
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom.,United Kingdom Dementia Research Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Melanie I Stefan
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom.,ZJU-UoE Institute, Zhejiang University, Haining, China
| | - Karl Emanuel Busch
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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22
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Kuo DH, De-Miguel FF, Heath-Heckman EAC, Szczupak L, Todd K, Weisblat DA, Winchell CJ. A tale of two leeches: Toward the understanding of the evolution and development of behavioral neural circuits. Evol Dev 2020; 22:471-493. [PMID: 33226195 DOI: 10.1111/ede.12358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 11/29/2022]
Abstract
In the animal kingdom, behavioral traits encompass a broad spectrum of biological phenotypes that have critical roles in adaptive evolution, but an EvoDevo approach has not been broadly used to study behavior evolution. Here, we propose that, by integrating two leech model systems, each of which has already attained some success in its respective field, it is possible to take on behavioral traits with an EvoDevo approach. We first identify the developmental changes that may theoretically lead to behavioral evolution and explain why an EvoDevo study of behavior is challenging. Next, we discuss the pros and cons of the two leech model species, Hirudo, a classic model for invertebrate neurobiology, and Helobdella, an emerging model for clitellate developmental biology, as models for behavioral EvoDevo research. Given the limitations of each leech system, neither is particularly strong for behavioral EvoDevo. However, the two leech systems are complementary in their technical accessibilities, and they do exhibit some behavioral similarities and differences. By studying them in parallel and together with additional leech species such as Haementeria, it is possible to explore the different levels of behavioral development and evolution.
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Affiliation(s)
- Dian-Han Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Francisco F De-Miguel
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, México City, México
| | | | - Lidia Szczupak
- Departamento de Fisiología Biología Molecular y Celular, Universidad de Buenos Aires, and IFIBYNE UBA-CONICET, Buenos Aires, Argentina
| | - Krista Todd
- Department of Neuroscience, Westminster College, Salt Lake City, Utah, USA
| | - David A Weisblat
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Christopher J Winchell
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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23
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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: 4.3] [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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24
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Abstract
For the first 25 years after the landmark 1974 paper that launched the field, most C. elegans biologists were content to think of their subjects as solitary creatures. C. elegans presented no shortage of fascinating biological problems, but some of the features that led Brenner to settle on this species-in particular, its free-living, self-fertilizing lifestyle-also seemed to reduce its potential for interesting social behavior. That perspective soon changed, with the last two decades bringing remarkable progress in identifying and understanding the complex interactions between worms. The growing appreciation that C. elegans behavior can only be meaningfully understood in the context of its ecology and evolution ensures that the coming years will see similarly exciting progress.
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Affiliation(s)
- Douglas S Portman
- Departments of Biomedical Genetics, Neuroscience, and Biology, Del Monte Institute for Neuroscience, University of Rochester, Rochester, NY, USA
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25
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Abstract
Microbes are ubiquitous in the natural environment of Caenorhabditis elegans. Bacteria serve as a food source for C. elegans but may also cause infection in the nematode host. The sensory nervous system of C. elegans detects diverse microbial molecules, ranging from metabolites produced by broad classes of bacteria to molecules synthesized by specific strains of bacteria. Innate recognition through chemosensation of bacterial metabolites or mechanosensation of bacteria can induce immediate behavioral responses. The ingestion of nutritive or pathogenic bacteria can modulate internal states that underlie long-lasting behavioral changes. Ingestion of nutritive bacteria leads to learned attraction and exploitation of the bacterial food source. Infection, which is accompanied by activation of innate immunity, stress responses, and host damage, leads to the development of aversive behavior. The integration of a multitude of microbial sensory cues in the environment is shaped by experience and context. Genetic, chemical, and neuronal studies of C. elegans behavior in the presence of bacteria have defined neural circuits and neuromodulatory systems that shape innate and learned behavioral responses to microbial cues. These studies have revealed the profound influence that host-microbe interactions have in governing the behavior of this simple animal host.
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Affiliation(s)
- Dennis H Kim
- Division of Infectious Diseases, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Steven W Flavell
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
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26
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Rapid Effects of Selection on Brain-wide Activity and Behavior. Curr Biol 2020; 30:3647-3656.e3. [PMID: 32763165 DOI: 10.1016/j.cub.2020.06.086] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/19/2020] [Accepted: 06/24/2020] [Indexed: 11/21/2022]
Abstract
Interindividual variation in behavior and brain activity is universal and provides substrates for natural selection [1-9]. Selective pressures shift the expression of behavioral traits at the population level [10, 11], but the accompanying changes of the underlying neural circuitry have rarely been identified [12, 13]. Selection likely acts through the genetic and/or epigenetic underpinnings of neural activity controlling the selected behavior [14]. Endocrine and neuromodulatory systems participate in behavioral diversity and could provide the substrate for evolutionary modifications [15-21]. Here, we examined brain-wide patterns of activity in larval zebrafish selectively bred over two generations for extreme differences in habituation of the acoustic startle response (ASR) [22]. The ASR is an evolutionarily conserved defensive behavior induced by strong acoustic/vibrational stimuli. ASR habituation shows great individual variability that is stable over days and heritable [4, 22]. Selection for high ASR habituation leads to stronger sound-evoked activation of ASR-processing brain areas. In contrast, animals selected for low habituation displayed stronger spontaneous activity in ASR-processing centers. Ablation of dopaminergic tyrosine hydroxylase (TH) neurons decreased ASR sensitivity. Independently selected ASR habituation lineages link the effect of behavioral selection to dopaminergic caudal hypothalamus (HC) neurons [23]. High ASR habituation co-segregated with decreased spontaneous swimming phenotypes, but visual startle responses were unaffected. Furthermore, high- and low-habituation larvae differed in stress responses as adults. Thus, selective pressure over a couple of generations on ASR habituation behavior is able to induce substantial differences in brain activity, carrying along additional behaviors as piggyback traits that might further affect fitness in the wild. VIDEO ABSTRACT.
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27
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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: 6.3] [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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28
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Noble LM, Miah A, Kaur T, Rockman MV. The Ancestral Caenorhabditis elegans Cuticle Suppresses rol-1. G3 (BETHESDA, MD.) 2020; 10:2385-2395. [PMID: 32423919 PMCID: PMC7341120 DOI: 10.1534/g3.120.401336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/09/2020] [Indexed: 12/30/2022]
Abstract
Genetic background commonly modifies the effects of mutations. We discovered that worms mutant for the canonical rol-1 gene, identified by Brenner in 1974, do not roll in the genetic background of the wild strain CB4856. Using linkage mapping, association analysis and gene editing, we determined that N2 carries an insertion in the collagen gene col-182 that acts as a recessive enhancer of rol-1 rolling. From population and comparative genomics, we infer the insertion is derived in N2 and related laboratory lines, likely arising during the domestication of Caenorhabditis elegans, and breaking a conserved protein. The ancestral version of col-182 also modifies the phenotypes of four other classical cuticle mutant alleles, and the effects of natural genetic variation on worm shape and locomotion. These results underscore the importance of genetic background and the serendipity of Brenner's choice of strain.
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Affiliation(s)
- Luke M Noble
- Institut de Biologie, École Normale Supérieure, CNRS 8197, Inserm U1024, PSL Research University, F-75005 Paris, France
| | - Asif Miah
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, 10003
| | - Taniya Kaur
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, 10003
| | - Matthew V Rockman
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, 10003
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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: 0.3] [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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Puchalt JC, Sánchez-Salmerón AJ, Ivorra E, Genovés Martínez S, Martínez R, Martorell Guerola P. Improving lifespan automation for Caenorhabditis elegans by using image processing and a post-processing adaptive data filter. Sci Rep 2020; 10:8729. [PMID: 32457411 PMCID: PMC7251096 DOI: 10.1038/s41598-020-65619-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/05/2020] [Indexed: 01/05/2023] Open
Abstract
Automated lifespan determination for C. elegans cultured in standard Petri dishes is challenging. Problems include occlusions of Petri dish edges, aggregation of worms, and accumulation of dirt (dust spots on lids) during assays, etc. This work presents a protocol for a lifespan assay, with two image-processing pipelines applied to different plate zones, and a new data post-processing method to solve the aforementioned problems. Specifically, certain steps in the culture protocol were taken to alleviate aggregation, occlusions, contamination, and condensation problems. This method is based on an active illumination system and facilitates automated image sequence analysis, does not need human threshold adjustments, and simplifies the techniques required to extract lifespan curves. In addition, two image-processing pipelines, applied to different plate zones, were employed for automated lifespan determination. The first image-processing pipeline was applied to a wall zone and used only pixel level information because worm size or shape features were unavailable in this zone. However, the second image-processing pipeline, applied to the plate centre, fused information at worm and pixel levels. Simple death event detection was used to automatically obtain lifespan curves from the image sequences that were captured once daily throughout the assay. Finally, a new post-processing method was applied to the extracted lifespan curves to filter errors. The experimental results showed that the errors in automated counting of live worms followed the Gaussian distribution with a mean of 2.91% and a standard deviation of ±12.73% per Petri plate. Post-processing reduced this error to 0.54 ± 8.18% per plate. The automated survival curve incurred an error of 4.62 ± 2.01%, while the post-process method reduced the lifespan curve error to approximately 2.24 ± 0.55%.
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Affiliation(s)
- Joan Carles Puchalt
- Universitat Politècnica de Valéncia, Instituto de Automática e Informática Industrial, Valencia, Spain
| | | | - Eugenio Ivorra
- Universitat Politècnica de Valéncia, Instituto de Automática e Informática Industrial, Valencia, Spain
| | | | - Roberto Martínez
- Cell Biology Laboratory/ADM Nutrition/Biopolis SL/Archer Daniels Midland, Paterna, Valencia, Spain
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31
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Abstract
Nervous systems allow animals to acutely respond and behaviorally adapt to changes and recurring patterns in their environment at multiple timescales-from milliseconds to years. Behavior is further shaped at intergenerational timescales by genetic variation, drift, and selection. This sophistication and flexibility of behavior makes it challenging to measure behavior consistently in individual subjects and to compare it across individuals. In spite of these challenges, careful behavioral observations in nature and controlled measurements in the laboratory, combined with modern technologies and powerful genetic approaches, have led to important discoveries about the way genetic variation shapes behavior. A critical mass of genes whose variation is known to modulate behavior in nature is finally accumulating, allowing us to recognize emerging patterns. In this review, we first discuss genetic mapping approaches useful for studying behavior. We then survey how variation acts at different levels-in environmental sensation, in internal neuronal circuits, and outside the nervous system altogether-and then discuss the sources and types of molecular variation linked to behavior and the mechanisms that shape such variation. We end by discussing remaining questions in the field.
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Affiliation(s)
- Natalie Niepoth
- Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; ,
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; ,
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32
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The complex genetic architecture of male mate choice evolution between Drosophila species. Heredity (Edinb) 2020; 124:737-750. [PMID: 32203250 DOI: 10.1038/s41437-020-0309-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 12/14/2022] Open
Abstract
Mate choice behaviors are among the most important reproductive isolating barriers in many animals. Little is known about the genetic basis of reproductively isolating behaviors, but examples to date provide evidence that they can have a simple genetic basis. However, it is unclear if these results indicate that individual genes with large effects are common, or are instead due to ascertainment biases. Here, we present the results of a QTL mapping study for the most important behavioral isolating barrier between Drosophila simulans and D. sechellia: male mate choice. Our QTL results initially suggested that differences in male mate choice may be due to a couple loci with large effects. However, as we divided the largest-effect QTL using stable introgression strains, we found evidence of multiple interacting loci. We further find that separate regions of the genome control different aspects of male choice. Taken together, our results suggest that the genetic architecture of mate choice behavior, in this case, is more complex than QTL mapping suggested, highlighting potential challenges to future mapping studies. We discuss the implications of these results as they relate to signal-receiver coevolution, mate choice, and reproductive isolation.
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33
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Demin KA, Lakstygal AM, Volgin AD, de Abreu MS, Genario R, Alpyshov ET, Serikuly N, Wang D, Wang J, Yan D, Wang M, Yang L, Hu G, Bytov M, Zabegalov KN, Zhdanov A, Harvey BH, Costa F, Rosemberg DB, Leonard BE, Fontana BD, Cleal M, Parker MO, Wang J, Song C, Amstislavskaya TG, Kalueff AV. Cross-species Analyses of Intra-species Behavioral Differences in Mammals and Fish. Neuroscience 2020; 429:33-45. [DOI: 10.1016/j.neuroscience.2019.12.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 12/28/2022]
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34
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Zhao Y, Long L, Wan J, Biliya S, Brady SC, Lee D, Ojemakinde A, Andersen EC, Vannberg FO, Lu H, McGrath PT. A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans. PLoS Genet 2020; 16:e1008606. [PMID: 32092052 PMCID: PMC7058356 DOI: 10.1371/journal.pgen.1008606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/05/2020] [Accepted: 01/11/2020] [Indexed: 01/02/2023] Open
Abstract
Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking. In this report, we study the genetic basis of adaptation of two strains of C. elegans to laboratory food sources using competition experiments on a panel of 89 recombinant inbred lines (RIL). Unexpectedly, we identified a single RIL with higher relative fitness than either of the parental strains. This strain also displayed a novel behavioral phenotype, resulting in higher propensity to explore bacterial lawns. Using bulk-segregant analysis and short-read resequencing of this RIL, we mapped the change in exploration behavior to a spontaneous, complex rearrangement of the rcan-1 gene that occurred during construction of the RIL panel. We resolved this rearrangement into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1 calcipressin gene, which has been implicated as a causal gene for Down syndrome. The genomic rearrangement in rcan-1 creates two complete and two truncated versions of the rcan-1 coding region, with a variety of modified 5’ and 3’ non-coding regions. While most copy-number variations (CNVs) are thought to act by increasing expression of duplicated genes, these changes to rcan-1 ultimately result in the reduction of its whole-body expression due to changes in the upstream regions. By backcrossing this rearrangement into a common genetic background to create a near isogenic line (NIL), we demonstrate that both the competitive advantage and exploration behavioral changes are linked to this complex genetic variant. This NIL strain does not phenocopy a strain containing an rcan-1 loss-of-function allele, which suggests that the residual expression of rcan-1 is necessary for its fitness effects. Our results demonstrate how colonization of new environments, such as those encountered in the laboratory, can create evolutionary pressure to modify gene function. This evolutionary mismatch can be resolved by an unexpectedly complex genetic change that simultaneously duplicates and diversifies a gene into two uniquely regulated genes. Our work shows how complex rearrangements can act to modify gene expression in ways besides increased gene dosage. Evolution acts on genetic variants that modify phenotypes that increase the likelihood of staying alive and passing on these genetic changes to subsequent generations (i.e. fitness). There is general interest in understanding the types of genetic variants that can increase fitness in specific environments. One route that fitness can be increased is through changes in behavior, such as finding new food sources. Here, we identify a spontaneous genetic change that increases exploration behavior and fitness of animals in laboratory environments. Interestingly, this genetic change is not a simple genetic change that deletes or changes the sequence of a protein product, but rather a complex structural variant that simultaneously duplicates the rcan-1 gene and also modifies its expression in a number of tissues. Our work demonstrates how a complex structural change can duplicate a gene, modify the DNA control regions that determine its cellular sites of action, and confer a fitness advantage that could lead to its spread in a population.
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Affiliation(s)
- Yuehui Zhao
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Lijiang Long
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jason Wan
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Shweta Biliya
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Shannon C. Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Akinade Ojemakinde
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Fredrik O. Vannberg
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Hang Lu
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Patrick T. McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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35
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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: 2.8] [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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36
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Crombie TA, Zdraljevic S, Cook DE, Tanny RE, Brady SC, Wang Y, Evans KS, Hahnel S, Lee D, Rodriguez BC, Zhang G, van der Zwagg J, Kiontke K, Andersen EC. Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations. eLife 2019; 8:50465. [PMID: 31793880 PMCID: PMC6927746 DOI: 10.7554/elife.50465] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/02/2019] [Indexed: 01/04/2023] Open
Abstract
Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral genetic diversity in the C. elegans species before human influence.
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Affiliation(s)
- Tim A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Shannon C Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Ye Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - Steffen Hahnel
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Briana C Rodriguez
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Joost van der Zwagg
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Karin Kiontke
- Department of Biology, New York University, New York, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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37
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Gloria-Soria A, Soghigian J, Kellner D, Powell JR. Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti. PLoS Negl Trop Dis 2019; 13:e0007930. [PMID: 31815934 PMCID: PMC6922456 DOI: 10.1371/journal.pntd.0007930] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 12/19/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022] Open
Abstract
The yellow fever mosquito (Aedes aegypti), is the primary vector of dengue, Zika, and chikungunya fever, among other arboviral diseases. It is also a popular laboratory model in vector biology due to its ease of rearing and manipulation in the lab. Established laboratory strains have been used worldwide in thousands of studies for decades. Laboratory evolution of reference strains and contamination among strains are potential severe problems that could dramatically change experimental outcomes and thus is a concern in vector biology. We analyzed laboratory and field colonies of Ae. aegypti and an Ae. aegypti-derived cell line (Aag2) using 12 microsatellites and ~20,000 SNPs to determine the extent of divergence among laboratory strains and relationships to their wild relatives. We found that 1) laboratory populations are less genetically variable than their field counterparts; 2) colonies bearing the same name obtained from different laboratories may be highly divergent; 3) present genetic composition of the LVP strain used as the genome reference is incompatible with its presumed origin; 4) we document changes in two wild caught colonies over ~16 generations of colonization; and 5) the Aag2 Ae. aegypti cell line has experienced minimal genetic changes within and across laboratories. These results illustrate the degree of variability within and among strains of Ae. aegypti, with implications for cross-study comparisons, and highlight the need of a common mosquito repository and the implementation of strain validation tools.
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Affiliation(s)
- Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
| | - John Soghigian
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
| | - David Kellner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
| | - Jeffrey R. Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
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38
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Beets I, Zhang G, Fenk LA, Chen C, Nelson GM, Félix MA, de Bono M. Natural Variation in a Dendritic Scaffold Protein Remodels Experience-Dependent Plasticity by Altering Neuropeptide Expression. Neuron 2019; 105:106-121.e10. [PMID: 31757604 PMCID: PMC6953435 DOI: 10.1016/j.neuron.2019.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 08/18/2019] [Accepted: 09/28/2019] [Indexed: 12/13/2022]
Abstract
The extent to which behavior is shaped by experience varies between individuals. Genetic differences contribute to this variation, but the neural mechanisms are not understood. Here, we dissect natural variation in the behavioral flexibility of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal regardless of previous O2 experience. We map that variation to a polymorphic dendritic scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2 at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation, an evolutionary process by which phenotypic flexibility in response to environmental variation is reset by genetic change. Behavioral flexibility varies across Caenorhabditis and C. elegans wild isolates A natural polymorphism in ARCP-1 underpins inter-individual variation in plasticity ARCP-1 is a dendritic scaffold protein localizing cGMP signaling machinery to cilia Disrupting ARCP-1 alters behavioral plasticity by changing neuropeptide expression
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Affiliation(s)
- Isabel Beets
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Gaotian Zhang
- Institut de Biologie de l'École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris 75005, France
| | - Lorenz A Fenk
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Changchun Chen
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Geoffrey M Nelson
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris 75005, France.
| | - Mario de Bono
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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39
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Abstract
Carbon dioxide (CO2) is an important sensory cue for many animals, including both parasitic and free-living nematodes. Many nematodes show context-dependent, experience-dependent and/or life-stage-dependent behavioural responses to CO2, suggesting that CO2 plays crucial roles throughout the nematode life cycle in multiple ethological contexts. Nematodes also show a wide range of physiological responses to CO2. Here, we review the diverse responses of parasitic and free-living nematodes to CO2. We also discuss the molecular, cellular and neural circuit mechanisms that mediate CO2 detection in nematodes, and that drive context-dependent and experience-dependent responses of nematodes to CO2.
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40
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Gimond C, Vielle A, Silva-Soares N, Zdraljevic S, McGrath PT, Andersen EC, Braendle C. Natural Variation and Genetic Determinants of Caenorhabditis elegans Sperm Size. Genetics 2019; 213:615-632. [PMID: 31395653 PMCID: PMC6781899 DOI: 10.1534/genetics.119.302462] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/04/2019] [Indexed: 01/28/2023] Open
Abstract
The diversity in sperm shape and size represents a powerful paradigm to understand how selection drives the evolutionary diversification of cell morphology. Experimental work on the sperm biology of the male-hermaphrodite nematode Caenorhabditis elegans has elucidated diverse factors important for sperm fertilization success, including the competitive superiority of larger sperm. Yet despite extensive research, the molecular mechanisms regulating C. elegans sperm size and the genetic basis underlying natural variation in sperm size remain unknown. To address these questions, we quantified male sperm size variation of a worldwide panel of 97 genetically distinct C. elegans strains, allowing us to uncover significant genetic variation in male sperm size. Aiming to characterize the molecular genetic basis of C. elegans male sperm size variation using a genome-wide association study, we did not detect any significant quantitative trait loci. We therefore focused on the genetic analysis of pronounced sperm size differences observed between recently diverged laboratory strains (N2 vs. LSJ1/2). Using mutants and quantitative complementation tests, we demonstrate that variation in the gene nurf-1 underlies the evolution of small sperm in the LSJ lineage. Given the previous discovery that this same nurf-1 variation was central for hermaphrodite laboratory adaptation, the evolution of reduced male sperm size in LSJ strains likely reflects a pleiotropic consequence. Together, our results provide a comprehensive quantification of natural variation in C. elegans sperm size and first insights into the genetic determinants of Caenorhabditis sperm size, pointing at an involvement of the NURF chromatin remodeling complex.
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Affiliation(s)
- Clotilde Gimond
- Université Côte d'Azur, CNRS, Inserm, IBV, Nice 06100, France
| | - Anne Vielle
- Université Côte d'Azur, CNRS, Inserm, IBV, Nice 06100, France
| | - Nuno Silva-Soares
- Université Côte d'Azur, CNRS, Inserm, IBV, Nice 06100, France
- Instituto Gulbenkian de Ciencia, 2780-156 Oeiras, Portugal
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Patrick T McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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41
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Bernstein MR, Zdraljevic S, Andersen EC, Rockman MV. Tightly linked antagonistic-effect loci underlie polygenic phenotypic variation in C. elegans. Evol Lett 2019; 3:462-473. [PMID: 31636939 PMCID: PMC6791183 DOI: 10.1002/evl3.139] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 08/23/2019] [Indexed: 12/31/2022] Open
Abstract
Recent work has provided strong empirical support for the classic polygenic model for trait variation. Population-based findings suggest that most regions of genome harbor variation affecting most traits. Here, we use the approach of experimental genetics to show that, indeed, most genomic regions carry variants with detectable effects on growth and reproduction in Caenorhabditis elegans populations sensitized by nickel stress. Nine of 15 adjacent intervals on the X chromosome, each encompassing ∼0.001 of the genome, have significant effects when tested individually in near-isogenic lines (NILs). These intervals have effects that are similar in magnitude to those of genome-wide significant loci that we mapped in a panel of recombinant inbred advanced intercross lines (RIAILs). If NIL-like effects were randomly distributed across the genome, the RIAILs would exhibit phenotypic variance that far exceeds the observed variance. However, the NIL intervals are arranged in a pattern that significantly reduces phenotypic variance relative to a random arrangement; adjacent intervals antagonize one another, cancelling each other's effects. Contrary to the expectation of small additive effects, our findings point to large-effect variants whose effects are masked by epistasis or linkage disequilibrium between alleles of opposing effect.
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Affiliation(s)
- Max R. Bernstein
- Department of Biology and Center for Genomics & Systems BiologyNew York UniversityNew YorkNew York10003
| | - Stefan Zdraljevic
- Molecular Biosciences and Interdisciplinary Biological Sciences ProgramNorthwestern UniversityEvanstonIllinois60208
| | - Erik C. Andersen
- Molecular Biosciences and Interdisciplinary Biological Sciences ProgramNorthwestern UniversityEvanstonIllinois60208
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics & Systems BiologyNew York UniversityNew YorkNew York10003
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42
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Xu W, Long L, Zhao Y, Stevens L, Felipe I, Munoz J, Ellis RE, McGrath PT. Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes. eLife 2019; 8:e48119. [PMID: 31498079 PMCID: PMC6752949 DOI: 10.7554/elife.48119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/05/2019] [Indexed: 12/13/2022] Open
Abstract
Genes can encode multiple isoforms, broadening their functions and providing a molecular substrate to evolve phenotypic diversity. Evolution of isoform function is a potential route to adapt to new environments. Here we show that de novo, beneficial alleles in the nurf-1 gene became fixed in two laboratory lineages of C. elegans after isolation from the wild in 1951, before methods of cryopreservation were developed. nurf-1 encodes an ortholog of BPTF, a large (>300 kD) multidomain subunit of the NURF chromatin remodeling complex. Using CRISPR-Cas9 genome editing and transgenic rescue, we demonstrate that in C. elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.D and NURF-1.B, which we call Yin and Yang, respectively) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation. Reproduction in hermaphrodites, which involves production of both sperm and oocytes, requires a balance of these opposing Yin and Yang isoforms. Transgenic rescue and genetic position of the fixed mutations suggest that different isoforms are modified in each laboratory strain. In a related clade of Caenorhabditis nematodes, the shared exons have duplicated, resulting in the split of the Yin and Yang isoforms into separate genes, each containing approximately 200 amino acids of duplicated sequence that has undergone accelerated protein evolution following the duplication. Associated with this duplication event is the loss of two additional nurf-1 transcripts, including the long-form transcript and a newly identified, highly expressed transcript encoded by the duplicated exons. We propose these lost transcripts are non-functional side products necessary to transcribe the Yin and Yang transcripts in the same cells. Our work demonstrates how gene sharing, through the production of multiple isoforms, can precede the creation of new, independent genes.
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Affiliation(s)
- Wen Xu
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Lijiang Long
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
- Interdisciplinary Graduate Program in Quantitative BiosciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Yuehui Zhao
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
| | - Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Irene Felipe
- Epithelial Carcinogenesis GroupSpanish National Cancer Research Center-CNIOMadridSpain
| | - Javier Munoz
- Proteomics Unit-ProteoRed-ISCIIISpanish National Cancer Research Center-CNIOMadridSpain
| | - Ronald E Ellis
- Department of Molecular BiologyRowan University School of Osteopathic MedicineStratfordUnited States
| | - Patrick T McGrath
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaUnited States
- Parker H. Petit Institute of Bioengineering and BioscienceGeorgia Institute of TechnologyAtlantaUnited States
- School of PhysicsGeorgia Institute of TechnologyAtlantaUnited States
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43
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Environmental Programming of Adult Foraging Behavior in C. elegans. Curr Biol 2019; 29:2867-2879.e4. [PMID: 31422888 DOI: 10.1016/j.cub.2019.07.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 05/26/2019] [Accepted: 07/12/2019] [Indexed: 11/22/2022]
Abstract
Foraging strategies should be tuned to the expected distribution of resources in the environment. Tuning can occur over generations and lead to genetic differences in innate foraging behavior or over shorter timescales within an individual's lifespan. Both genetically encoded and experience-based strategies are implemented by neural circuits that respond to environmental cues and track internal states. Caenorhabditis elegans exhibit both between-strain genetic differences and within-strain plasticity in foraging. In individuals, changes in foraging are usually short term and based on recent experience. Here, we tested whether developmental experience could permanently alter foraging. We found that, in most wild strains, early-life starvation led to "cautious" foraging strategies, in which exploration is reduced, and these behavioral changes are associated with altered dynamics in a locomotory circuit. Possessing either the derived (domestication-associated) or ancestral allele of the neuroglobin glb-5 determines foraging plasticity. Overall, we show that C. elegans exhibit adaptive developmental plasticity that affects multiple aspects of foraging behavior and leads to changes in a core navigation circuit and that innate foraging traits and plasticity in those traits are genetically separable. VIDEO ABSTRACT.
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44
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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: 6.0] [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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45
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Stegeman GW, Baird SE, Ryu WS, Cutter AD. Genetically Distinct Behavioral Modules Underlie Natural Variation in Thermal Performance Curves. G3 (BETHESDA, MD.) 2019; 9:2135-2151. [PMID: 31048400 PMCID: PMC6643873 DOI: 10.1534/g3.119.400043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/30/2019] [Indexed: 01/01/2023]
Abstract
Thermal reaction norms pervade organismal traits as stereotyped responses to temperature, a fundamental environmental input into sensory and physiological systems. Locomotory behavior represents an especially plastic read-out of animal response, with its dynamic dependence on environmental stimuli presenting a challenge for analysis and for understanding the genomic architecture of heritable variation. Here we characterize behavioral reaction norms as thermal performance curves for the nematode Caenorhabditis briggsae, using a collection of 23 wild isolate genotypes and 153 recombinant inbred lines to quantify the extent of genetic and plastic variation in locomotory behavior to temperature changes. By reducing the dimensionality of the multivariate phenotypic response with a function-valued trait framework, we identified genetically distinct behavioral modules that contribute to the heritable variation in the emergent overall behavioral thermal performance curve. Quantitative trait locus mapping isolated regions on Chromosome II associated with locomotory activity at benign temperatures and Chromosome V loci related to distinct aspects of sensitivity to high temperatures, with each quantitative trait locus explaining up to 28% of trait variation. These findings highlight how behavioral responses to environmental inputs as thermal reaction norms can evolve through independent changes to genetically distinct modular components of such complex phenotypes.
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Affiliation(s)
| | - Scott E Baird
- Department of Biology, Wright State University, Dayton, Ohio, 45435
| | - William S Ryu
- Department of Physics, University of Toronto
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S3B2, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto
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46
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Patel DS, Xu N, Lu H. Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans. Lab Anim (NY) 2019; 48:207-216. [PMID: 31217565 DOI: 10.1038/s41684-019-0326-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/17/2019] [Indexed: 11/09/2022]
Abstract
Deep phenotyping is an emerging conceptual paradigm and experimental approach aimed at measuring and linking many aspects of a phenotype to understand its underlying biology. To date, deep phenotyping has been applied mostly in cultured cells and used less in multicellular organisms. However, in the past decade, it has increasingly been recognized that deep phenotyping could lead to a better understanding of how genetics, environment and stochasticity affect the development, physiology and behavior of an organism. The nematode Caenorhabditis elegans is an invaluable model system for studying how genes affect a phenotypic trait, and new technologies have taken advantage of the worm's physical attributes to increase the throughput and informational content of experiments. Coupling of these technical advancements with computational and analytical tools has enabled a boom in deep-phenotyping studies of C. elegans. In this Review, we highlight how these new technologies and tools are digging into the biological origins of complex, multidimensional phenotypes.
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Affiliation(s)
- Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nan Xu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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47
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Burga A, Ben-David E, Lemus Vergara T, Boocock J, Kruglyak L. Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk. Nat Commun 2019; 10:2680. [PMID: 31213597 PMCID: PMC6582151 DOI: 10.1038/s41467-019-10636-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/16/2019] [Indexed: 02/03/2023] Open
Abstract
Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We use ceX-QTL to map a drug resistance locus with high resolution. We also map differences in gene expression in live worms and discovered that mutations in the co-chaperone sti-1 upregulate the transcription of HSP-90. Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals.
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Affiliation(s)
- Alejandro Burga
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
| | - Eyal Ben-David
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Tzitziki Lemus Vergara
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - James Boocock
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Leonid Kruglyak
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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48
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Stegeman GW, Medina D, Cutter AD, Ryu WS. Neuro-genetic plasticity of Caenorhabditis elegans behavioral thermal tolerance. BMC Neurosci 2019; 20:26. [PMID: 31182018 PMCID: PMC6558720 DOI: 10.1186/s12868-019-0510-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/03/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Animal responses to thermal stimuli involve intricate contributions of genetics, neurobiology and physiology, with temperature variation providing a pervasive environmental factor for natural selection. Thermal behavior thus exemplifies a dynamic trait that requires non-trivial phenotypic summaries to appropriately capture the trait in response to a changing environment. To characterize the deterministic and plastic components of thermal responses, we developed a novel micro-droplet assay of nematode behavior that permits information-dense summaries of dynamic behavioral phenotypes as reaction norms in response to increasing temperature (thermal tolerance curves, TTC). RESULTS We found that C. elegans TTCs shift predictably with rearing conditions and developmental stage, with significant differences between distinct wildtype genetic backgrounds. Moreover, after screening TTCs for 58 C. elegans genetic mutant strains, we determined that genes affecting thermosensation, including cmk-1 and tax-4, potentially play important roles in the behavioral control of locomotion at high temperature, implicating neural decision-making in TTC shape rather than just generalized physiological limits. However, expression of the transient receptor potential ion channel TRPA-1 in the nervous system is not sufficient to rescue rearing-dependent plasticity in TTCs conferred by normal expression of this gene, indicating instead a role for intestinal signaling involving TRPA-1 in the adaptive plasticity of thermal performance. CONCLUSIONS These results implicate nervous system and non-nervous system contributions to behavior, in addition to basic cellular physiology, as key mediators of evolutionary responses to selection from temperature variation in nature.
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Affiliation(s)
- Gregory W Stegeman
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Denise Medina
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Department of Physics, University of Toronto, Toronto, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - William S Ryu
- Department of Physics, University of Toronto, Toronto, Canada.
- Donnelly Centre, University of Toronto, Toronto, ON, M5S3E1, Canada.
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49
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Biology is the root of variability: cautionary tales in Caenorhabditis elegans biology. Biochem Soc Trans 2019; 47:887-896. [PMID: 31127069 DOI: 10.1042/bst20190001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Abstract
Reproducibility is critical for the standardization, interpretation, and progression of research. However, many factors increase variability and reduce reproducibility. In Caenorhabditis elegans research, there are many possible causes of variability that may explain why experimental outcomes sometimes differ between laboratories and between experiments. Factors contributing to experimental variability include the genetic background of both C. elegans and its bacterial diet, differences in media composition, intergenerational and transgenerational effects that may be carried over for generations, and the use of chemicals or reagents that may have unexpected consequences. This review summarizes sources of variability in C. elegans research and serves to identify laboratory practices that could influence reproducibility.
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50
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Ding SS, Schumacher LJ, Javer AE, Endres RG, Brown AEX. Shared behavioral mechanisms underlie C. elegans aggregation and swarming. eLife 2019; 8:e43318. [PMID: 31021320 PMCID: PMC6522220 DOI: 10.7554/elife.43318] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/19/2019] [Indexed: 11/13/2022] Open
Abstract
In complex biological systems, simple individual-level behavioral rules can give rise to emergent group-level behavior. While collective behavior has been well studied in cells and larger organisms, the mesoscopic scale is less understood, as it is unclear which sensory inputs and physical processes matter a priori. Here, we investigate collective feeding in the roundworm C. elegans at this intermediate scale, using quantitative phenotyping and agent-based modeling to identify behavioral rules underlying both aggregation and swarming-a dynamic phenotype only observed at longer timescales. Using fluorescence multi-worm tracking, we quantify aggregation in terms of individual dynamics and population-level statistics. Then we use agent-based simulations and approximate Bayesian inference to identify three key behavioral rules for aggregation: cluster-edge reversals, a density-dependent switch between crawling speeds, and taxis towards neighboring worms. Our simulations suggest that swarming is simply driven by local food depletion but otherwise employs the same behavioral mechanisms as the initial aggregation.
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Affiliation(s)
- Siyu Serena Ding
- Instititue of Clinical SciencesImperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
| | - Linus J Schumacher
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Avelino E Javer
- Instititue of Clinical SciencesImperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
| | - Robert G Endres
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - André EX Brown
- Instititue of Clinical SciencesImperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
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