1
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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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2
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Crombie TA, Chikuturudzi C, Cook DE, Andersen EC. An automated approach to quantify chemotaxis index in C. elegans. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000567. [PMID: 35647500 PMCID: PMC9136590 DOI: 10.17912/micropub.biology.000567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]
Abstract
Chemotaxis assays are used extensively to study behavioral responses of Caenorhabditis nematodes to environmental cues. These assays result in a chemotaxis index (CI) that denotes the behavioral response of a population of nematodes to a particular compound and can range from 1 (maximum attraction) to -1 (maximum avoidance). Traditional chemotaxis assays have low throughput because researchers must manually setup experimental populations and score CIs. Here, we describe an automated methodology that increases throughput by using liquid-handling robots to setup experimental populations and a custom image analysis package, ct, to automate the scoring of CIs from plate images.
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Affiliation(s)
- Timothy A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Chido Chikuturudzi
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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3
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Lansdon P, Carlson M, Ackley BD. Wild-type Caenorhabditis elegans isolates exhibit distinct gene expression profiles in response to microbial infection. BMC Genomics 2022; 23:229. [PMID: 35321659 PMCID: PMC8943956 DOI: 10.1186/s12864-022-08455-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/28/2022] [Indexed: 11/20/2022] Open
Abstract
The soil-dwelling nematode Caenorhabditis elegans serves as a model system to study innate immunity against microbial pathogens. C. elegans have been collected from around the world, where they, presumably, adapted to regional microbial ecologies. Here we use survival assays and RNA-sequencing to better understand how two isolates from disparate climates respond to pathogenic bacteria. We found that, relative to N2 (originally isolated in Bristol, UK), CB4856 (isolated in Hawaii), was more susceptible to the Gram-positive microbe, Staphylococcus epidermidis, but equally susceptible to Staphylococcus aureus as well as two Gram-negative microbes, Providencia rettgeri and Pseudomonas aeruginosa. We performed transcriptome analysis of infected worms and found gene-expression profiles were considerably different in an isolate-specific and microbe-specific manner. We performed GO term analysis to categorize differential gene expression in response to S. epidermidis. In N2, genes that encoded detoxification enzymes and extracellular matrix proteins were significantly enriched, while in CB4856, genes that encoded detoxification enzymes, C-type lectins, and lipid metabolism proteins were enriched, suggesting they have different responses to S. epidermidis, despite being the same species. Overall, discerning gene expression signatures in an isolate by pathogen manner can help us to understand the different possibilities for the evolution of immune responses within organisms.
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Affiliation(s)
- Patrick Lansdon
- Department of Molecular Biosciences, University of Kansas, 5004 Haworth Hall, 1200 Sunnyside Ave, KS, 66045, Lawrence, USA
| | - Maci Carlson
- Department of Molecular Biosciences, University of Kansas, 5004 Haworth Hall, 1200 Sunnyside Ave, KS, 66045, Lawrence, USA
| | - Brian D Ackley
- Department of Molecular Biosciences, University of Kansas, 5004 Haworth Hall, 1200 Sunnyside Ave, KS, 66045, Lawrence, USA.
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4
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Chen AJ, Zuazo C, Mellman K, Chandra R, L'Etoile N. C. elegans show Preference for Pseudomonas mendocina (MSPm1) and Proteus mirabilis ( P. mirabilis sp?) , and Repulsion to Pseudomonas lurida (MYb11); Growth on Pseudomonas mendocina (MSPm1) Increases Attraction to 2-nonanone. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000535. [PMID: 35622520 PMCID: PMC9010113 DOI: 10.17912/micropub.biology.000535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 03/05/2022] [Indexed: 11/06/2022]
Abstract
C. elegans’
experiences and microbiome have been shown to shape its responses to certain stimuli; a recent study found that
C. elegans
grown on
Providencia alcalifaciens
JUb39 exhibited increased attraction to that same growth bacteria while also lowered repulsion to the odor 1-octanol (O’Donnell et al. 2020). This prompted us to ask whether other strains of bacteria could likewise alter
C. elegans’
responses to bacterial food and volatile chemicals. So, to expand upon current knowledge, we cultured wild-type
C. elegans
(N2) on an unidentified
Escherichia coli
(
E. coli
sp?),
Pseudomonas mendocina
(MSPm1),
Pseudomonas lurida
(MYb11),
Stenotrophomonas maltophilia
(JUb19), or
Proteus mirabilis
strain (
P. mirabilis
sp?). After several generations, we examined how their choice of bacterial food was affected. In addition, we looked at their response to the olfactory stimuli 2-butanone; 2,3-butanedione; 2,3-pentanedione; and 2-nonanone, as well as their response to the gustatory stimulus sodium chloride. Interestingly, we found that growth on any of these bacterial strains led to their bacterial preferences and behavioral responses to 2-butanone; 2,3-pentanedione; diacetyl; and sodium chloride remaining unchanged. However, we also saw that
C. elegans
showed a preference for MSPm1 and
P. mirabilis
sp? to HB101, and HB101 to
MYb11. Furthermore, worms that are grown on MSPm1 showed stronger attraction to a 1:10 dilution of 2-nonanone (AWB-sensed odorant) as compared to worms grown on the other bacterial strains.
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Affiliation(s)
- Alec J Chen
- Department of Cell and Tissue Biology, University of California, San Francisco
,
Johns Hopkins Undergraduate
| | - Carlos Zuazo
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Katie Mellman
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Rashmi Chandra
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Noelle L'Etoile
- Department of Cell and Tissue Biology, University of California, San Francisco
,
Correspondence to: Noelle L'Etoile (
)
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5
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The Role of Serratomolide-like Amino Lipids Produced by Bacteria of Genus Serratia in Nematicidal Activity. Pathogens 2022; 11:pathogens11020198. [PMID: 35215141 PMCID: PMC8880026 DOI: 10.3390/pathogens11020198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/13/2022] [Accepted: 01/29/2022] [Indexed: 02/04/2023] Open
Abstract
Bursaphelenchus xylophilus, also known as pinewood nematode (PWN), is the pathogenic agent of pine wilt disease (PWD), which affects pine trees around the world. Infection spread globally through international wood commerce and locally by vector beetles, threatening the wood world economy. As climate changes, more countries are becoming susceptible to PWD and, to prevent disease spread and limit economic and ecological losses, better knowledge about this pathogenic agent is needed. Serratia strains, present in the endophytic community of pine trees and carried by PWN, may play an important role in PWD. This work aimed to better understand the interaction between Serratia strains and B. xylophilus and to assess the nematicidal potential of serratomolide-like molecules produced by Serratia strains. Serrawettin gene presence was evaluated in selected Serratia strains. Mortality tests were performed with bacteria supernatants, and extracted amino lipids, against Caenorhabditis elegans (model organism) and B. xylophilus to determine their nematicidal potential. Attraction tests were performed with C. elegans. Concentrated supernatants of Serratia strains with serratamolide-like lipopeptides were able to kill more than 77% of B. xylophilus after 72 h. Eight specific amino lipids showed a high nematicidal activity against B. xylophilus. We conclude that, for some Serratia strains, their supernatants and specific amino lipids showed nematicidal activity against B. xylophilus.
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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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7
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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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8
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Khanna A, Sellegounder D, Kumar J, Chamoli M, Vargas M, Chinta SJ, Rane A, Nelson C, Peiris TH, Brem R, Andersen J, Lithgow G, Kapahi P. Trimethylamine modulates dauer formation, neurodegeneration, and lifespan through tyra-3/daf-11 signaling in Caenorhabditis elegans. Aging Cell 2021; 20:e13351. [PMID: 33819374 PMCID: PMC8135002 DOI: 10.1111/acel.13351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 02/10/2021] [Accepted: 03/05/2021] [Indexed: 11/27/2022] Open
Abstract
In the nematode Caenorhabditis elegans, signals derived from bacteria in the diet, the animal's major nutrient source, can modulate both behavior and healthspan. Here we describe a dual role for trimethylamine (TMA), a human gut flora metabolite, which acts as a nutrient signal and a neurotoxin. TMA and its associated metabolites are produced by the human gut microbiome and have been suggested to serve as risk biomarkers for diabetes and cardiovascular diseases. We demonstrate that the tyramine receptor TYRA-3, a conserved G protein-coupled receptor (GPCR), is required to sense TMA and mediate its responses. TMA activates guanylyl cyclase DAF-11 signaling through TYRA-3 in amphid neurons (ASK) and ciliated neurons (BAG) to mediate food-sensing behavior. Bacterial mutants deficient in TMA production enhance dauer formation, extend lifespan, and are less preferred as a food source. Increased levels of TMA lead to neural damage in models of Parkinson's disease and shorten lifespan. Our results reveal conserved signaling pathways modulated by TMA in C. elegans that are likely to be relevant for its effects in mammalian systems.
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Affiliation(s)
- Amit Khanna
- Buck Institute for Research on Aging Novato CA USA
- Dovetail Genomics LLC Scotts Valley CA USA
| | | | | | | | | | - Shankar J. Chinta
- Buck Institute for Research on Aging Novato CA USA
- Touro University California Vallejo CA USA
| | - Anand Rane
- Buck Institute for Research on Aging Novato CA USA
| | | | | | - Rachel Brem
- Buck Institute for Research on Aging Novato CA USA
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9
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White PS, Arslan D, Kim D, Penley M, Morran L. Host genetic drift and adaptation in the evolution and maintenance of parasite resistance. J Evol Biol 2021; 34:845-851. [PMID: 33783870 DOI: 10.1111/jeb.13785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 03/22/2021] [Indexed: 01/17/2023]
Abstract
Host-parasite interactions may often be subject to opposing evolutionary forces, which likely influence the evolutionary trajectories of both partners. Natural selection and genetic drift are two major evolutionary forces that act in host and parasite populations. Further, population size is a significant determinant of the relative strengths of these forces. In small populations, drift may undermine the persistence of beneficial alleles, potentially impeding host adaptation to parasites. Here, we investigate two questions: (a) can selection pressure for increased resistance in small, susceptible host populations overcome the effects of drift and (b) can resistance be maintained in small host populations? To answer these questions, we experimentally evolved the host Caenorhabditis elegans against its bacterial parasite, Serratia marcescens, for 13 host generations. We found that strong selection favouring increased host resistance was insufficient to counteract drift in small populations, resulting in persistently high host mortality. Additionally, in small populations of resistant hosts, we found that selection for the maintenance of resistance is not always sufficient to curb the loss of resistance. We compared these results with selection in large host populations. We found that initially resistant, large host populations were able to maintain high levels of resistance. Likewise, initially susceptible, large host populations were able to gain resistance to the parasite. These results show that strong selection pressure for survival is not always sufficient to counteract drift. In consideration of C. elegans natural population dynamics, we suggest that drift may often impede selection in nature.
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Affiliation(s)
- P Signe White
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Danial Arslan
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA, USA
| | - David Kim
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA, USA
| | - McKenna Penley
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA, USA
| | - Levi Morran
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA, USA
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10
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Bourgeois JS, Smith CM, Ko DC. These Are the Genes You're Looking For: Finding Host Resistance Genes. Trends Microbiol 2021; 29:346-362. [PMID: 33004258 PMCID: PMC7969353 DOI: 10.1016/j.tim.2020.09.006] [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: 06/13/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host-bacterial interactions at the genome-wide level, including screens that harness CRISPR/Cas9 genome editing, natural genetic variation, proteomics, and transcriptomics. We report on the merits, limitations, and findings of these innovative screens and discuss their complementary nature. Finally, we speculate on future innovation as we continue to progress through the postgenomic era and towards deeper mechanistic insight and clinical applications.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Duke Human Vaccine Institute, School of Medicine, Duke University Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA.
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11
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Interpopulational Variations of Odorant-Binding Protein Expression in the Black Cutworm Moth, Agrotis ipsilon. INSECTS 2020; 11:insects11110798. [PMID: 33202803 PMCID: PMC7696954 DOI: 10.3390/insects11110798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 11/28/2022]
Abstract
Simple Summary Odorant-binding proteins (OBPs) are small soluble transporter proteins that are believed to play a key role in insect olfaction. However, there is an emerging set of data that shows a role in insecticide resistance for similar families of binding proteins. The black cutworm Agrotis ipsilon is a migrant species of moth known to feed on multiple types of crops (polyphagous) worldwide. It is therefore likely that the olfactory system of this species can be modulated to adapt to different environments. We compared gene expression between American and European continental populations of the moth. We found continental-specific expression of antennal binding protein X (ABPX) and general odorant-binding protein 2 (GOBP2), suggesting a function of these proteins in migration, environment recognition, crop change and adaptation that are required for a polyphagous species such as A. ipsilon. Abstract A long-range migrant species of moth (Agrotis ipsilon) has served as a model to compare the expression profiles of antennal proteins between different continental populations. Our results showed that the American and French populations of the black cutworm moth, A. ipsilon, expressed the same odorant-binding proteins (OBPs), but apparently in different levels. Electrophoretic analysis of antennal protein profiles and reverse transcription polymerase chain reaction using RNA as a template showed significant differences between the two populations in the expression of antennal binding protein-X (ABPX) and general odorant-binding protein-2 (GOBP2). However, the two A. ipsilon populations showed no differences in RNA levels coding for pheromone binding proteins (PBPs), suggesting that the expression of generalist OBPs is population-specific and could be affected by specific odor and/or chemical changes in external environmental conditions. To support the role of ABPX and GOBP2 with expression, the role of ABPX and GOBP2 is discussed in regard to odor detection, memorization and/or degradation of toxic chemical insecticides.
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12
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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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13
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Sterken MG, Bevers RPJ, Volkers RJM, Riksen JAG, Kammenga JE, Snoek BL. Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans. Front Genet 2020; 11:501376. [PMID: 33240309 PMCID: PMC7670075 DOI: 10.3389/fgene.2020.501376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/13/2020] [Indexed: 01/11/2023] Open
Abstract
The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in Caenorhabditis elegans using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the cis- and 40% of the trans-eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60-93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for cis vs. trans eQTL and that the environment affects the eQTL micro-architecture.
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Affiliation(s)
- Mark G. Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Roel P. J. Bevers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Rita J. M. Volkers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands
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14
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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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15
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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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16
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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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17
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Huang Y, Kammenga JE. Genetic Variation in Caenorhabditis elegans Responses to Pathogenic Microbiota. Microorganisms 2020; 8:E618. [PMID: 32344661 PMCID: PMC7232262 DOI: 10.3390/microorganisms8040618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/30/2022] Open
Abstract
The bacterivorous nematode Caenorhabditis elegans is an important model species for understanding genetic variation of complex traits. So far, most studies involve axenic laboratory settings using Escherichia coli as the sole bacterial species. Over the past decade, however, investigations into the genetic variation of responses to pathogenic microbiota have increasingly received attention. Quantitative genetic analyses have revealed detailed insight into loci, genetic variants, and pathways in C. elegans underlying interactions with bacteria, microsporidia, and viruses. As various quantitative genetic platforms and resources like C. elegans Natural Diversity Resource (CeNDR) and Worm Quantitative Trait Loci (WormQTL) have been developed, we anticipate that expanding C. elegans research along the lines of genetic variation will be a treasure trove for opening up new insights into genetic pathways and gene functionality of microbiota interactions.
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Affiliation(s)
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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18
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Velagapudi P, Ghoubrial R, Shah R, Ghali H, Haas M, Patel KS, Riddell A, Blanar CA, Smith RP. A potential tradeoff between feeding rate and aversive learning determines intoxication in a Caenorhabditis elegans host-pathogen system. Microbes Infect 2020; 22:340-348. [PMID: 32014589 DOI: 10.1016/j.micinf.2020.01.002] [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: 06/03/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 11/29/2022]
Abstract
Despite being the first line of defense against infection, little is known about how host-pathogen interactions determine avoidance. Caenorhabditis elegans can become infected by chemoattractant-producing bacteria through ingestion. The worms can learn to associate these chemoattractants with harm through aversive learning. As a result, the worms will avoid the pathogen. Evolutionary constraints have likely shaped the attraction, intoxication and learning dynamics between bacteria and C. elegans, but these have not been explored. Using bacteria engineered to express an acylhomoserine lactone chemoattractant and a nematicidal protein, we explored how manipulating the amount of attractant produced by the bacteria affects learning and intoxication in mixed stage populations of C. elegans. We found that increasing the production rate of the chemoattractant increased the feeding rate in C. elegans, but decreased the time required for C. elegans to learn to avoid the chemoattractant. Learning generally coincided with a decreased feeding rate. We also observed that the percentage of intoxicated worms was maximized at intermediate production rates of the attractant. We propose that interactions between attractant driven feeding rate and aversive learning are likely responsible for this trend. Our results increase our understanding of behavioral avoidance in C. elegans and have implications in understanding host-pathogen dynamics that shape avoidance.
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Affiliation(s)
- Pallavi Velagapudi
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Rachel Ghoubrial
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Ratnavi Shah
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Helana Ghali
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Meghan Haas
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Krunal S Patel
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Ashleigh Riddell
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Christopher A Blanar
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA
| | - Robert P Smith
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, 33314, USA.
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19
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White PS, Choi A, Pandey R, Menezes A, Penley M, Gibson AK, de Roode J, Morran L. Host heterogeneity mitigates virulence evolution. Biol Lett 2020; 16:20190744. [PMID: 31992149 PMCID: PMC7013476 DOI: 10.1098/rsbl.2019.0744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 01/21/2023] Open
Abstract
Parasites often infect genetically diverse host populations, and the evolutionary trajectories of parasite populations may be shaped by levels of host heterogeneity. Mixed genotype host populations, compared to homogeneous host populations, can reduce parasite prevalence and potentially reduce rates of parasite adaptation due to trade-offs associated with adapting to specific host genotypes. Here, we used experimental evolution to select for increased virulence in populations of the bacterial parasite Serratia marcescens exposed to either heterogeneous or homogeneous populations of Caenorhabditis elegans. We found that parasites exposed to heterogeneous host populations evolved significantly less virulence than parasites exposed to homogeneous host populations over several hundred bacterial generations. Thus, host heterogeneity impeded parasite adaptation to host populations. While we detected trade-offs in virulence evolution, parasite adaptation to two specific host genotypes also resulted in modestly increased virulence against the reciprocal host genotypes. These results suggest that parasite adaptation to heterogeneous host populations may be impeded by both trade-offs and a reduction in the efficacy of selection as different host genotypes exert different selective pressures on a parasite population.
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Affiliation(s)
- P. Signe White
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Angela Choi
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Rishika Pandey
- Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA
| | - Arthur Menezes
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - McKenna Penley
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Amanda K. Gibson
- Department of Biology, College and Graduate School of Arts and Sciences, University of Virginia, Charlottesville, VA 22904, USA
| | - Jacobus de Roode
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Levi Morran
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
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20
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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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21
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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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22
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White PS, Penley MJ, Tierney ARP, Soper DM, Morran LT. Dauer life stage of Caenorhabditis elegans induces elevated levels of defense against the parasite Serratia marcescens. Sci Rep 2019; 9:11575. [PMID: 31399616 PMCID: PMC6688991 DOI: 10.1038/s41598-019-47969-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/23/2019] [Indexed: 01/17/2023] Open
Abstract
Host-parasite research often focuses on a single host life stage, yet different life stages may exhibit different defenses. The nematode Caenorhabditis elegans has an alternate dispersal life stage, dauer. Despite dauer's importance in nature, we know little of how it responds to parasites. Previous research indicates that non-dauer C. elegans prefer to consume the virulent bacterial parasite, Serratia marcescens, when given a choice between the parasite and benign Escherichia coli. Here, we compared the preferences of dauer individuals from six strains of C. elegans to the preferences of other life stages. We found that dauer individuals exhibited reduced preference for S. marcescens, and dauers from some strains preferred E. coli to S. marcescens. In addition to testing food preference, a mechanism of parasite avoidance, we also measured host mortality rates after direct parasite exposure to determine if life stage also altered host survival. Overall, dauer individuals exhibited reduced mortality rates. However, dauer versus non-dauer larvae mortality rates also varied significantly by host strain. Collectively, we found evidence of dauer-induced parasite avoidance and reduced mortality in the presence of a parasite, but these effects were strain-specific. These results demonstrate the importance of host life stage and genotype when assessing infection dynamics.
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Affiliation(s)
- P Signe White
- Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, GA, 30322, USA.
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| | - McKenna J Penley
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Aimee R Paulk Tierney
- Microbiology and Molecular Genetics Graduate Program, Emory University, Atlanta, GA, 30322, USA
| | - Deanna M Soper
- Biology Department, University of Dallas, Irving, TX, 75062, USA
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
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23
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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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24
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Benowitz KM, Coleman JM, Matzkin LM. Assessing the Architecture of Drosophila mojavensis Locomotor Evolution with Bulk Segregant Analysis. G3 (BETHESDA, MD.) 2019; 9:1767-1775. [PMID: 30926724 PMCID: PMC6505136 DOI: 10.1534/g3.119.400036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/22/2019] [Indexed: 11/24/2022]
Abstract
Behavior is frequently predicted to be especially important for evolution in novel environments. If these predictions are accurate, there might be particular patterns of genetic architecture associated with recently diverged behaviors. Specifically, it has been predicted that behaviors linked to population divergence should be underpinned by a few genes of relatively large effect, compared to architectures of intrapopulation behavioral variation, which is considered to be highly polygenic. More mapping studies of behavioral variation between recently diverged populations are needed to continue assessing the generality of these predictions. Here, we used a bulk segregant mapping approach to dissect the genetic architecture of a locomotor trait that has evolved between two populations of the cactophilic fly Drosophila mojavensis We created an F8 mapping population of 1,500 individuals from advanced intercross lines and sequenced the 10% of individuals with the highest and lowest levels of locomotor activity. Using three alternative statistical approaches, we found strong evidence for two relatively large-effect QTL that is localized in a region homologous to a region of densely packed behavior loci in Drosophila melanogaster, suggesting that clustering of behavior genes may display relatively deep evolutionary conservation. Broadly, our data are most consistent with a polygenic architecture, though with several loci explaining a high proportion of variation in comparison to similar behavioral traits. We further note the presence of several antagonistic QTL linked to locomotion and discuss these results in light of theories regarding behavioral evolution and the effect size and direction of QTL for diverging traits in general.
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Affiliation(s)
- Kyle M Benowitz
- Department of Entomology, University of Arizona, Tucson, AZ 85721
| | - Joshua M Coleman
- Department of Entomology, University of Arizona, Tucson, AZ 85721
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville AL 35899
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ 85721
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, Tucson, AZ 85721
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25
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Worthy SE, Rojas GL, Taylor CJ, Glater EE. Identification of Odor Blend Used by Caenorhabditis elegans for Pathogen Recognition. Chem Senses 2019; 43:169-180. [PMID: 29373666 PMCID: PMC6018680 DOI: 10.1093/chemse/bjy001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Animals have evolved specialized pathways to detect appropriate food sources and avoid harmful ones. Caenorhabditis elegans can distinguish among the odors of various species of bacteria, its major food source, but little is known about what specific chemical cue or combination of chemical cues C. elegans uses to detect and recognize different microbes. Here, we examine the strong innate attraction of C. elegans for the odor of the pathogenic bacterium, Serratia marcescens. This initial attraction likely facilitates ingestion and infection of the C. elegans host. Using solid-phase microextraction and gas chromatography coupled with mass spectrometry, we identify 5 volatile odors released by S. marcescens and identify those that are attractive to C. elegans. We use genetic methods to show that the amphid chemosensory neuron, AWCON, senses both S. marcescens-released 2-butanone and acetone and drives attraction to S. marcescens. In C. elegans, pairing a single odorant with food deprivation results in a reduced attractive response for that specific odor. We find that pairing the natural odor of S. marcescens with food deprivation results in a reduced attraction for the natural odor of S. marcescens and a similar reduced attraction for the synthetic blend of acetone and 2-butanone. This result indicates that only 2 odorants represent the more complex odor bouquet of S. marcescens. Although bacterial-released volatiles have long been known to be attractive to C. elegans, this study defines for the first time specific volatile cues that represent a particular bacterium to C. elegans.
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Affiliation(s)
| | - German L Rojas
- Department of Neuroscience, Pomona College, Claremont, CA, USA
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26
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Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses. Genetics 2018; 210:1509-1525. [PMID: 30341085 PMCID: PMC6283156 DOI: 10.1534/genetics.118.301311] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/16/2018] [Indexed: 01/25/2023] Open
Abstract
Phenotypic complexity is caused by the contributions of environmental factors and multiple genetic loci, interacting or acting independently. Studies of yeast and Arabidopsis often find that the majority of natural variation across phenotypes is attributable to independent additive quantitative trait loci (QTL). Detected loci in these organisms explain most of the estimated heritable variation. By contrast, many heritable components underlying phenotypic variation in metazoan models remain undetected. Before the relative impacts of additive and interactive variance components on metazoan phenotypic variation can be dissected, high replication and precise phenotypic measurements are required to obtain sufficient statistical power to detect loci contributing to this missing heritability. Here, we used a panel of 296 recombinant inbred advanced intercross lines of Caenorhabditis elegans and a high-throughput fitness assay to detect loci underlying responses to 16 different toxins, including heavy metals, chemotherapeutic drugs, pesticides, and neuropharmaceuticals. Using linkage mapping, we identified 82 QTL that underlie variation in responses to these toxins, and predicted the relative contributions of additive loci and genetic interactions across various growth parameters. Additionally, we identified three genomic regions that impact responses to multiple classes of toxins. These QTL hotspots could represent common factors impacting toxin responses. We went further to generate near-isogenic lines and chromosome substitution strains, and then experimentally validated these QTL hotspots, implicating additive and interactive loci that underlie toxin-response variation.
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27
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Woodruff GC, Phillips PC. Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps. BMC Ecol 2018; 18:26. [PMID: 30129423 PMCID: PMC6102938 DOI: 10.1186/s12898-018-0182-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biotic interactions are ubiquitous and require information from ecology, evolutionary biology, and functional genetics in order to be understood. However, study systems that are amenable to investigations across such disparate fields are rare. Figs and fig wasps are a classic system for ecology and evolutionary biology with poor functional genetics; Caenorhabditis elegans is a classic system for functional genetics with poor ecology. In order to help bridge these disciplines, here we describe the natural history of a close relative of C. elegans, Caenorhabditis inopinata, that is associated with the fig Ficus septica and its pollinating Ceratosolen wasps. RESULTS To understand the natural context of fig-associated Caenorhabditis, fresh F. septica figs from four Okinawan islands were sampled, dissected, and observed under microscopy. C. inopinata was found in all islands where F. septica figs were found. C.i nopinata was routinely found in the fig interior and almost never observed on the outside surface. C. inopinata was only found in pollinated figs, and C. inopinata was more likely to be observed in figs with more foundress pollinating wasps. Actively reproducing C. inopinata dominated early phase figs, whereas late phase figs with emerging wasp progeny harbored C. inopinata dauer larvae. Additionally, C. inopinata was observed dismounting from Ceratosolen pollinating wasps that were placed on agar plates. C. inopinata was not found on non-pollinating, parasitic Philotrypesis wasps. Finally, C. inopinata was only observed in F. septica figs among five Okinawan Ficus species sampled. CONCLUSION These are the first detailed field observations of C. inopinata, and they suggest a natural history where this species proliferates in early phase F. septica figs and disperses from late phase figs on Ceratosolen pollinating fig wasps. While consistent with other examples of nematode diversification in the fig microcosm, the fig and wasp host specificity of C. inopinata is highly divergent from the life histories of its close relatives and frames hypotheses for future investigations. This natural co-occurrence of the fig/fig wasp and C. inopinata study systems sets the stage for an integrated research program that can help to explain the evolution of interspecific interactions.
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Affiliation(s)
- Gavin C Woodruff
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, Tsukuba, Japan.
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
| | - Patrick C Phillips
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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Worthy SE, Haynes L, Chambers M, Bethune D, Kan E, Chung K, Ota R, Taylor CJ, Glater EE. Identification of attractive odorants released by preferred bacterial food found in the natural habitats of C. elegans. PLoS One 2018; 13:e0201158. [PMID: 30036396 PMCID: PMC6056031 DOI: 10.1371/journal.pone.0201158] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/10/2018] [Indexed: 01/26/2023] Open
Abstract
Food choice is critical for survival because organisms must choose food that is edible and nutritious and avoid pathogenic food. Many organisms, including the nematode C. elegans, use olfaction to detect and distinguish among food sources. C. elegans exhibits innate preferences for the odors of different bacterial species. However, little is known about the preferences of C. elegans for bacterial strains isolated from their natural environment as well as the attractive volatile compounds released by preferred natural bacteria isolates. We tested food odor preferences of C. elegans for non-pathogenic bacteria found in their natural habitats. We found that C. elegans showed a preference for the odor of six of the eight tested bacterial isolates over its standard food source, E. coli HB101. Using solid-phase microextraction and gas chromatography coupled with mass spectrometry, we found that four of six attractive bacterial isolates (Alcaligenes sp. JUb4, Providenica sp. JUb5, Providencia sp. JUb39, and Flavobacteria sp. JUb43) released isoamyl alcohol, a well-studied C. elegans attractant, while both non-attractive isolates (Raoultella sp. JUb38 and Acinetobacter sp. JUb68) released very low or non-detectable amounts of isoamyl alcohol. In conclusion, we find that isoamyl alcohol is likely an ethologically relevant odor that is released by some attractive bacterial isolates in the natural environment of C. elegans.
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Affiliation(s)
- Soleil E. Worthy
- Department of Chemistry, Pomona College, Claremont, California, United States of America
| | - Lillian Haynes
- Department of Biology, Harvey Mudd College, Claremont, California, United States of America
| | - Melissa Chambers
- Department of Neuroscience, Pomona College, Claremont, California, United States of America
| | - Danika Bethune
- Department of Neuroscience, Pomona College, Claremont, California, United States of America
| | - Emily Kan
- Department of Neuroscience, Pomona College, Claremont, California, United States of America
| | - Kevin Chung
- Department of Neuroscience, Pomona College, Claremont, California, United States of America
| | - Ryan Ota
- Department of Neuroscience, Pomona College, Claremont, California, United States of America
| | - Charles J. Taylor
- Department of Chemistry, Pomona College, Claremont, California, United States of America
| | - Elizabeth E. Glater
- Department of Neuroscience, Pomona College, Claremont, California, United States of America
- * E-mail:
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Use of a Sibling Subtraction Method for Identifying Causal Mutations in Caenorhabditis elegans by Whole-Genome Sequencing. G3-GENES GENOMES GENETICS 2018; 8:669-678. [PMID: 29237702 PMCID: PMC5919755 DOI: 10.1534/g3.117.300135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome sequencing (WGS) is an indispensable tool for identifying causal mutations obtained from genetic screens. To reduce the number of causal mutation candidates typically uncovered by WGS, Caenorhabditis elegans researchers have developed several strategies. One involves crossing N2-background mutants to the polymorphic Hawaiian (HA) strain, which can be used to simultaneously identify mutant strain variants and obtain high-density mapping information. This approach, however, is not well suited for uncovering mutations in complex genetic backgrounds, and HA polymorphisms can alter phenotypes. Other approaches make use of DNA variants present in the initial background or introduced by mutagenesis. This information is used to implicate genomic regions with high densities of DNA lesions that persist after backcrossing, but these methods can provide lower resolution than HA mapping. To identify suppressor mutations using WGS, we developed an approach termed the sibling subtraction method (SSM). This method works by eliminating variants present in both mutants and their nonmutant siblings, thus greatly reducing the number of candidates. We used this method with two members of the C. elegans NimA-related kinase family, nekl-2 and nekl-3. Combining weak aphenotypic alleles of nekl-2 and nekl-3 leads to penetrant molting defects and larval arrest. We isolated ∼50 suppressors of nekl-2; nekl-3 synthetic lethality using F1 clonal screening methods and a peel-1–based counterselection strategy. When applied to five of the suppressors, SSM led to only one to four suppressor candidates per strain. Thus SSM is a powerful approach for identifying causal mutations in any genetic background and provides an alternative to current methods.
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GIBSON AMANDAK, MORRAN LEVIT. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites. J Nematol 2018. [DOI: 10.21307/jofnem-2017-083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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31
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Gibson AK, Morran LT. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites. J Nematol 2017; 49:357-372. [PMID: 29353923 PMCID: PMC5770282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 06/07/2023] Open
Abstract
Many of the outstanding questions in disease ecology and evolution call for combining observation of natural host-parasite populations with experimental dissection of interactions in the field and the laboratory. The "rewilding" of model systems holds great promise for this endeavor. Here, we highlight the potential for development of the nematode Caenorhabditis elegans and its close relatives as a model for the study of disease ecology and evolution. This powerful laboratory model was disassociated from its natural habitat in the 1960s. Today, studies are uncovering that lost natural history, with several natural parasites described since 2008. Studies of these natural Caenorhabditis-parasite interactions can reap the benefits of the vast array of experimental and genetic tools developed for this laboratory model. In this review, we introduce the natural parasites of C. elegans characterized thus far and discuss resources available to study them, including experimental (co)evolution, cryopreservation, behavioral assays, and genomic tools. Throughout, we present avenues of research that are interesting and feasible to address with caenorhabditid nematodes and their natural parasites, ranging from the maintenance of outcrossing to the community dynamics of host-associated microbes. In combining natural relevance with the experimental power of a laboratory supermodel, these fledgling host-parasite systems can take on fundamental questions in evolutionary ecology of disease.
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Affiliation(s)
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, GA 30322
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32
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Penley MJ, Ha GT, Morran LT. Evolution of Caenorhabditis elegans host defense under selection by the bacterial parasite Serratia marcescens. PLoS One 2017; 12:e0181913. [PMID: 28792961 PMCID: PMC5549931 DOI: 10.1371/journal.pone.0181913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 04/21/2017] [Indexed: 01/13/2023] Open
Abstract
Parasites can impose strong selection on hosts. In response, some host populations have adapted via the evolution of defenses that prevent or impede infection by parasites. However, host populations have also evolved life history shifts that maximize host fitness despite infection. Outcrossing and self-fertilization can have contrasting effects on evolutionary trajectories of host populations. While selfing and outcrossing are known to affect the rate at which host populations adapt in response to parasites, these mating systems may also influence the specific traits that underlie adaptation to parasites. Here, we determined the role of evolved host defense versus altered life history,in mixed mating (selfing and outcrossing) and obligately outcrossing C. elegans host populations after experimental evolution with the bacterial parasite, S. marcescens. Similar to previous studies, we found that both mixed mating and obligately outcrossing host populations adapted to S. marcescens exposure, and that the obligately outcrossing populations exhibited the greatest rates of adaptation. Regardless of the host population mating system, exposure to parasites did not significantly alter reproductive timing or total fecundity over the course of experimental evolution. However, both mixed mating and obligately outcrossing host populations exhibited significantly reduced mortality rates in the presence of the parasite after experimental evolution. Therefore, adaptation in both the mixed mating and obligately outcrossing populations was driven, at least in part, by the evolution of increased host defense and not changes in host life history. Thus, the host mating system altered the rate of adaptation, but not the nature of adaptive change in the host populations.
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Affiliation(s)
- McKenna J. Penley
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Giang T. Ha
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Levi T. Morran
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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33
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Host mating system and coevolutionary dynamics shape the evolution of parasite avoidance in Caenorhabditis elegans host populations. Parasitology 2017; 145:724-730. [DOI: 10.1017/s0031182017000804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractHosts exhibit a variety of defence mechanisms against parasites, including avoidance. Both host–parasite coevolutionary dynamics and the host mating system can alter the evolutionary trajectories of populations. Does the nature of host–parasite interactions and the host mating system affect the mechanisms that evolve to confer host defence? In a previous experimental evolution study, mixed mating and obligately outcrossing Caenorhabditis elegans host populations adapted to either coevolving or static Serratia marcescens parasite populations. Here, we assessed parasite avoidance as a mechanism underlying host adaptation. We measured host feeding preference for the coevolved and static parasites vs preference for Escherichia coli, to assess the evolution of avoidance behaviour within our experiment. We found that mixed mating host populations evolved a preference for E. coli relative to the static parasite strain; therefore, the hosts evolved parasite avoidance as a defence. However, mixed mating hosts did not exhibit E. coli preference when exposed to coevolved parasites, so avoidance cannot account for host adaptation to coevolving parasites. Further, the obligately outcrossing host populations did not exhibit parasite avoidance in the presence of either static or coevolved parasites. Therefore, both the nature of host–parasite interactions and the host mating system shaped the evolution of host defence.
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34
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Teotónio H, Estes S, Phillips PC, Baer CF. Experimental Evolution with Caenorhabditis Nematodes. Genetics 2017; 206:691-716. [PMID: 28592504 PMCID: PMC5499180 DOI: 10.1534/genetics.115.186288] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 03/07/2017] [Indexed: 12/17/2022] Open
Abstract
The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host-pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative.
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Affiliation(s)
- Henrique Teotónio
- Institut de Biologie de l´École Normale Supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre Nationnal de la Recherche Scientifique Unité Mixte de Recherche 8197, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Suzanne Estes
- Department of Biology, Portland State University, Oregon 97201
| | - Patrick C Phillips
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, Oregon 97403, and
| | - Charles F Baer
- Department of Biology, and
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida 32611
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35
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Large EE, Padmanabhan R, Watkins KL, Campbell RF, Xu W, McGrath PT. Modeling of a negative feedback mechanism explains antagonistic pleiotropy in reproduction in domesticated Caenorhabditis elegans strains. PLoS Genet 2017; 13:e1006769. [PMID: 28493873 PMCID: PMC5444864 DOI: 10.1371/journal.pgen.1006769] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 05/25/2017] [Accepted: 04/21/2017] [Indexed: 11/29/2022] Open
Abstract
Most biological traits and common diseases have a strong but complex genetic basis, controlled by large numbers of genetic variants with small contributions to a trait or disease risk. The effect-size of most genetic variants is not absolute and is instead dependent upon multiple factors such as the age and genetic background of an organism. In order to understand the mechanistic basis of these changes, we characterized heritable trait differences between two domesticated strains of C. elegans. We previously identified a major effect locus, caused in part by a mutation in a component of the NURF chromatin remodeling complex, that regulates reproductive output in an age-dependent manner. The effect-size of this locus changes from positive to negative over the course of an animal’s reproductive lifespan. Here, we use a previously published macroscale model of the egg-laying rate in C. elegans to show that time-dependent effect-size is explained by an unequal use of sperm combined with negative feedback between sperm and ovulation rate. We validate key predictions of this model with controlled mating experiments and quantification of oogenesis and sperm use. Incorporation of this model into QTL mapping allows us to identify and partition new QTLs into specific aspects of the egg-laying process. Finally, we show how epistasis between two genetic variants is predicted by this modeling as a consequence of the unequal use of sperm. This work demonstrates how modeling of multicellular communication systems can improve our ability to predict and understand the role of genetic variation on a complex phenotype. Negative autoregulatory feedback loops, common in transcriptional regulation, could play an important role in modifying genetic architecture in other traits. Complex traits are influenced by the individual effects of genetic variants in addition to the interactions of the variants with the environment, age, and each other. While complex genetic architectures are ubiquitous in natural traits, little is known about the causal mechanisms that create their complex genetic architectures. Here we identify an example of age-dependent genetic architecture controlling the rate and timing of reproduction in the hermaphroditic nematode C. elegans. We use computational modeling to demonstrate how age-dependent genetic architecture can arise as a consequence of two factors: hormonal feedback on oocytes mediated by major sperm protein (MSP) released by sperm stored in the spermatheca and life history differences in sperm use caused by genetic variants. Our work also suggests how antagonistic pleiotropy can emerge from multicellular feedback systems.
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Affiliation(s)
- Edward E. Large
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Raghavendra Padmanabhan
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Kathie L. Watkins
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Richard F. Campbell
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Wen Xu
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Patrick T. McGrath
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
- * E-mail:
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36
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Schulenburg H, Félix MA. The Natural Biotic Environment of Caenorhabditis elegans. Genetics 2017; 206:55-86. [PMID: 28476862 PMCID: PMC5419493 DOI: 10.1534/genetics.116.195511] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 01/05/2023] Open
Abstract
Organisms evolve in response to their natural environment. Consideration of natural ecological parameters are thus of key importance for our understanding of an organism's biology. Curiously, the natural ecology of the model species Caenorhabditis elegans has long been neglected, even though this nematode has become one of the most intensively studied models in biological research. This lack of interest changed ∼10 yr ago. Since then, an increasing number of studies have focused on the nematode's natural ecology. Yet many unknowns still remain. Here, we provide an overview of the currently available information on the natural environment of C. elegans We focus on the biotic environment, which is usually less predictable and thus can create high selective constraints that are likely to have had a strong impact on C. elegans evolution. This nematode is particularly abundant in microbe-rich environments, especially rotting plant matter such as decomposing fruits and stems. In this environment, it is part of a complex interaction network, which is particularly shaped by a species-rich microbial community. These microbes can be food, part of a beneficial gut microbiome, parasites and pathogens, and possibly competitors. C. elegans is additionally confronted with predators; it interacts with vector organisms that facilitate dispersal to new habitats, and also with competitors for similar food environments, including competitors from congeneric and also the same species. Full appreciation of this nematode's biology warrants further exploration of its natural environment and subsequent integration of this information into the well-established laboratory-based research approaches.
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Affiliation(s)
- Hinrich Schulenburg
- Zoological Institute, Christian-Albrechts Universitaet zu Kiel, 24098 Kiel, Germany
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale Supérieure, L'université de Recherche Paris Sciences et Lettres, 75005, France
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37
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Khanna A, Kumar J, Vargas MA, Barrett L, Katewa S, Li P, McCloskey T, Sharma A, Naudé N, Nelson C, Brem R, Killilea DW, Mooney SD, Gill M, Kapahi P. A genome-wide screen of bacterial mutants that enhance dauer formation in C. elegans. Sci Rep 2016; 6:38764. [PMID: 27958277 PMCID: PMC5153853 DOI: 10.1038/srep38764] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/10/2016] [Indexed: 11/09/2022] Open
Abstract
Molecular pathways involved in dauer formation, an alternate larval stage that allows Caenorhabditis elegans to survive adverse environmental conditions during development, also modulate longevity and metabolism. The decision to proceed with reproductive development or undergo diapause depends on food abundance, population density, and temperature. In recent years, the chemical identities of pheromone signals that modulate dauer entry have been characterized. However, signals derived from bacteria, the major source of nutrients for C. elegans, remain poorly characterized. To systematically identify bacterial components that influence dauer formation and aging in C. elegans, we utilized the individual gene deletion mutants in E. coli (K12). We identified 56 diverse E. coli deletion mutants that enhance dauer formation in an insulin-like receptor mutant (daf-2) background. We describe the mechanism of action of a bacterial mutant cyaA, that is defective in the production of cyclic AMP, which extends lifespan and enhances dauer formation through the modulation of TGF-β (daf-7) signaling in C. elegans. Our results demonstrate the importance of bacterial components in influencing developmental decisions and lifespan in C. elegans. Furthermore, we demonstrate that C. elegans is a useful model to study bacterial-host interactions.
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Affiliation(s)
- Amit Khanna
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - Jitendra Kumar
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - Misha A Vargas
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - LaKisha Barrett
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - Subhash Katewa
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - Patrick Li
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - Tom McCloskey
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - Amit Sharma
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - Nicole Naudé
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | | | - Rachel Brem
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
| | - David W Killilea
- Nutrition &Metabolism Center, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington 98195, USA
| | - Matthew Gill
- Department of Metabolism &Aging, The Scripps Research Institute- Scripps Florida, Jupiter, Florida, 33458, USA
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, USA
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Ballestriero F, Nappi J, Zampi G, Bazzicalupo P, Di Schiavi E, Egan S. Caenorhabditis elegans employs innate and learned aversion in response to bacterial toxic metabolites tambjamine and violacein. Sci Rep 2016; 6:29284. [PMID: 27384057 PMCID: PMC4935850 DOI: 10.1038/srep29284] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 06/14/2016] [Indexed: 12/19/2022] Open
Abstract
Bacteriovorus eukaryotes such as nematodes are one of the major natural predators of bacteria. In their defense bacteria have evolved a number of strategies to avoid predation, including the production of deterrent or toxic metabolites, however little is known regarding the response of predators towards such bacterial defenses. Here we use the nematode C. elegans as a model to study a predators’ behavioral response towards two toxic bacterial metabolites, tambjamine YP1 and violacein. We found that C. elegans displays an innate avoidance behavior towards tambjamine YP1, however requires previous exposure to violacein before learning to avoid this metabolite. The learned avoidance of violacein is specific, reversible, is mediated via the nematode olfactory apparatus (aversive olfactory learning) and is reduced in the absence of the neurotransmitter serotonin. These multiple strategies to evade bacterial toxic metabolites represent a valuable behavioral adaptation allowing bacteriovorus predators to distinguish between good and bad food sources, thus contributing to the understanding of microbial predator-prey interactions.
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Affiliation(s)
- Francesco Ballestriero
- School of Biological, Earth and Environmental Science and Centre for Marine Bio-Innovation, University of New South Wales, Australia
| | - Jadranka Nappi
- School of Biological, Earth and Environmental Science and Centre for Marine Bio-Innovation, University of New South Wales, Australia
| | - Giuseppina Zampi
- Institute of Biosciences and BioResources, National Research Council, Naples, Italy
| | - Paolo Bazzicalupo
- Institute of Biosciences and BioResources, National Research Council, Naples, Italy.,Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Elia Di Schiavi
- Institute of Biosciences and BioResources, National Research Council, Naples, Italy.,Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Suhelen Egan
- School of Biological, Earth and Environmental Science and Centre for Marine Bio-Innovation, University of New South Wales, Australia
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39
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Nakad R, Snoek LB, Yang W, Ellendt S, Schneider F, Mohr TG, Rösingh L, Masche AC, Rosenstiel PC, Dierking K, Kammenga JE, Schulenburg H. Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1. BMC Genomics 2016; 17:280. [PMID: 27066825 PMCID: PMC4827197 DOI: 10.1186/s12864-016-2603-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 03/25/2016] [Indexed: 01/22/2023] Open
Abstract
Background The invertebrate immune system comprises physiological mechanisms, physical barriers and also behavioral responses. It is generally related to the vertebrate innate immune system and widely believed to provide nonspecific defense against pathogens, whereby the response to different pathogen types is usually mediated by distinct signalling cascades. Recent work suggests that invertebrate immune defense can be more specific at least at the phenotypic level. The underlying genetic mechanisms are as yet poorly understood. Results We demonstrate in the model invertebrate Caenorhabditis elegans that a single gene, a homolog of the mammalian neuropeptide Y receptor gene, npr-1, mediates contrasting defense phenotypes towards two distinct pathogens, the Gram-positive Bacillus thuringiensis and the Gram-negative Pseudomonas aeruginosa. Our findings are based on combining quantitative trait loci (QTLs) analysis with functional genetic analysis and RNAseq-based transcriptomics. The QTL analysis focused on behavioral immune defense against B. thuringiensis, using recombinant inbred lines (RILs) and introgression lines (ILs). It revealed several defense QTLs, including one on chromosome X comprising the npr-1 gene. The wildtype N2 allele for the latter QTL was associated with reduced defense against B. thuringiensis and thus produced an opposite phenotype to that previously reported for the N2 npr-1 allele against P. aeruginosa. Analysis of npr-1 mutants confirmed these contrasting immune phenotypes for both avoidance behavior and nematode survival. Subsequent transcriptional profiling of C. elegans wildtype and npr-1 mutant suggested that npr-1 mediates defense against both pathogens through p38 MAPK signaling, insulin-like signaling, and C-type lectins. Importantly, increased defense towards P. aeruginosa seems to be additionally influenced through the induction of oxidative stress genes and activation of GATA transcription factors, while the repression of oxidative stress genes combined with activation of Ebox transcription factors appears to enhance susceptibility to B. thuringiensis. Conclusions Our findings highlight the role of a single gene, npr-1, in fine-tuning nematode immune defense, showing the ability of the invertebrate immune system to produce highly specialized and potentially opposing immune responses via single regulatory genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2603-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rania Nakad
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - L Basten Snoek
- Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Wentao Yang
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Sunna Ellendt
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Franziska Schneider
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Timm G Mohr
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Lone Rösingh
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Anna C Masche
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Philip C Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, 24098, Kiel, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, University of Kiel, 24098, Kiel, Germany.
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40
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Yen CA, Curran SP. Gene-diet interactions and aging in C. elegans. Exp Gerontol 2016; 86:106-112. [PMID: 26924670 DOI: 10.1016/j.exger.2016.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/16/2016] [Accepted: 02/24/2016] [Indexed: 02/06/2023]
Abstract
Diet is the most variable aspect of life history, as most individuals have a large diversity of food choices, varying in the type and amount that they ingest. In the short-term, diet can affect metabolism and energy levels. However, in the long run, the net deficiency or excess of calories from diet can influence the progression and severity of age-related diseases. An old and yet still debated question is: how do specific dietary choices impact health- and lifespan? It is clear that genetics can play a critical role - perhaps just as important as diet choices. For example, poor diet in combination with genetic susceptibility can lead to metabolic disorders, such as obesity and type 2 diabetes. Recent work in Caenorhabditis elegans has identified the existence of diet-gene pairs, where the consequence of mutating a specific gene is only realized on specific diets. Many core metabolic pathways are conserved from worm to human. Although only a handful of these diet-gene pairs has been characterized, there are potentially hundreds, if not thousands, of such interactions, which may explain the variability in the rates of aging in humans and the incidence and severity of age-related diseases.
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Affiliation(s)
- Chia An Yen
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States
| | - Sean P Curran
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States; University of Southern California, Davis School of Gerontology, United States.
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A Powerful New Quantitative Genetics Platform, Combining Caenorhabditis elegans High-Throughput Fitness Assays with a Large Collection of Recombinant Strains. G3-GENES GENOMES GENETICS 2015; 5:911-20. [PMID: 25770127 PMCID: PMC4426375 DOI: 10.1534/g3.115.017178] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The genetic variants underlying complex traits are often elusive even in powerful model organisms such as Caenorhabditis elegans with controlled genetic backgrounds and environmental conditions. Two major contributing factors are: (1) the lack of statistical power from measuring the phenotypes of small numbers of individuals, and (2) the use of phenotyping platforms that do not scale to hundreds of individuals and are prone to noisy measurements. Here, we generated a new resource of 359 recombinant inbred strains that augments the existing C. elegans N2xCB4856 recombinant inbred advanced intercross line population. This new strain collection removes variation in the neuropeptide receptor gene npr-1, known to have large physiological and behavioral effects on C. elegans and mitigates the hybrid strain incompatibility caused by zeel-1 and peel-1, allowing for identification of quantitative trait loci that otherwise would have been masked by those effects. Additionally, we optimized highly scalable and accurate high-throughput assays of fecundity and body size using the COPAS BIOSORT large particle nematode sorter. Using these assays, we identified quantitative trait loci involved in fecundity and growth under normal growth conditions and after exposure to the herbicide paraquat, including independent genetic loci that regulate different stages of larval growth. Our results offer a powerful platform for the discovery of the genetic variants that control differences in responses to drugs, other aqueous compounds, bacterial foods, and pathogenic stresses.
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42
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Petersen C, Dirksen P, Schulenburg H. Why we need more ecology for genetic models such as C. elegans. Trends Genet 2015; 31:120-7. [PMID: 25577479 DOI: 10.1016/j.tig.2014.12.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/28/2022]
Abstract
Functional information about the large majority of the genes is still lacking in the classical eukaryotic model species Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus. Because many of these genes are likely to be important in natural settings, considering explicit ecological information should increase our knowledge of gene function. Using C. elegans as an example, we discuss the importance of biotic factors as a driving force in shaping the composition and structure of the nematode genome. We highlight examples for which consideration of ecological information and natural variation have been key to the identification of novel, unexpected gene functions, and use these examples to define future research avenues for the classical genetic model taxa.
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Affiliation(s)
- Carola Petersen
- Evolutionary Ecology and Genetics, University of Kiel, 24098 Kiel, Germany
| | - Philipp Dirksen
- Evolutionary Ecology and Genetics, University of Kiel, 24098 Kiel, Germany
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43
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Green JWM, Stastna JJ, Orbidans HE, Harvey SC. Highly polygenic variation in environmental perception determines dauer larvae formation in growing populations of Caenorhabditis elegans. PLoS One 2014; 9:e112830. [PMID: 25393108 PMCID: PMC4231163 DOI: 10.1371/journal.pone.0112830] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 10/16/2014] [Indexed: 11/25/2022] Open
Abstract
Background Determining how complex traits are genetically controlled is a requirement if we are to predict how they evolve and how they might respond to selection. This requires understanding how distinct, and often more simple, life history traits interact and change in response to environmental conditions. In order to begin addressing such issues, we have been analyzing the formation of the developmentally arrested dauer larvae of Caenorhabditis elegans under different conditions. Results We find that 18 of 22 previously identified quantitative trait loci (QTLs) affecting dauer larvae formation in growing populations, assayed by determining the number of dauer larvae present at food patch exhaustion, can be recovered under various environmental conditions. We also show that food patch size affects both the ability to detect QTLs and estimates of effect size, and demonstrate that an allele of nath-10 affects dauer larvae formation in growing populations. To investigate the component traits that affect dauer larvae formation in growing populations we map, using the same introgression lines, QTLs that affect dauer larvae formation in response to defined amounts of pheromone. This identifies 36 QTLs, again demonstrating the highly polygenic nature of the genetic variation underlying dauer larvae formation. Conclusions These data indicate that QTLs affecting the number of dauer larvae at food exhaustion in growing populations of C. elegans are highly reproducible, and that nearly all can be explained by variation affecting dauer larvae formation in response to defined amounts of pheromone. This suggests that most variation in dauer larvae formation in growing populations is a consequence of variation in the perception of the food and pheromone environment (i.e. chemosensory variation) and in the integration of these cues.
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Affiliation(s)
- James W. M. Green
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Jana J. Stastna
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Helen E. Orbidans
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Simon C. Harvey
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
- * E-mail:
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44
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Meisel JD, Kim DH. Behavioral avoidance of pathogenic bacteria by Caenorhabditis elegans. Trends Immunol 2014; 35:465-70. [PMID: 25240986 DOI: 10.1016/j.it.2014.08.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 08/25/2014] [Accepted: 08/25/2014] [Indexed: 12/25/2022]
Abstract
The simple animal host Caenorhabditis elegans utilizes its nervous system to respond to diverse microbial cues, and can engage in a protective behavioral avoidance response to environmental pathogens. This behavior bears hallmarks of an immune response, with sensors and recognition systems that trigger a protective response following a learning experience. Neuronal circuits required for aversive learning have been defined, revealing conserved signaling modules with dual roles in immunity and neuronal responses to pathogenic bacteria. Identification of natural polymorphisms that modulate avoidance behavior has enabled an improved understanding of host-microbe interactions at the molecular level. We review here these findings and discuss how the microbial cues and host responses defined in C. elegans may provide insight into evolutionarily diverse host-microbe interactions.
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Affiliation(s)
- Joshua D Meisel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dennis H Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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45
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Snoek LB, Orbidans HE, Stastna JJ, Aartse A, Rodriguez M, Riksen JAG, Kammenga JE, Harvey SC. Widespread genomic incompatibilities in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2014; 4:1813-23. [PMID: 25128438 PMCID: PMC4199689 DOI: 10.1534/g3.114.013151] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/17/2014] [Indexed: 01/18/2023]
Abstract
In the Bateson-Dobzhansky-Muller (BDM) model of speciation, incompatibilities emerge from the deleterious interactions between alleles that are neutral or advantageous in the original genetic backgrounds, i.e., negative epistatic effects. Within species such interactions are responsible for outbreeding depression and F2 (hybrid) breakdown. We sought to identify BDM incompatibilities in the nematode Caenorhabditis elegans by looking for genomic regions that disrupt egg laying; a complex, highly regulated, and coordinated phenotype. Investigation of introgression lines and recombinant inbred lines derived from the isolates CB4856 and N2 uncovered multiple incompatibility quantitative trait loci (QTL). These QTL produce a synthetic egg-laying defective phenotype not seen in CB4856 and N2 nor in other wild isolates. For two of the QTL regions, results are inconsistent with a model of pairwise interaction between two loci, suggesting that the incompatibilities are a consequence of complex interactions between multiple loci. Analysis of additional life history traits indicates that the QTL regions identified in these screens are associated with effects on other traits such as lifespan and reproduction, suggesting that the incompatibilities are likely to be deleterious. Taken together, these results indicate that numerous BDM incompatibilities that could contribute to reproductive isolation can be detected and mapped within C. elegans.
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Affiliation(s)
- L Basten Snoek
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Helen E Orbidans
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
| | - Jana J Stastna
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
| | - Aafke Aartse
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Miriam Rodriguez
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Simon C Harvey
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
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46
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Gelperin A. Comparative chemosensory cognition. Front Behav Neurosci 2014; 8:190. [PMID: 24904341 PMCID: PMC4033254 DOI: 10.3389/fnbeh.2014.00190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 05/07/2014] [Indexed: 01/07/2023] Open
Affiliation(s)
- Alan Gelperin
- Department of Molecular Biology, Princeton Neuroscience Institute, Princeton University, Princeton NJ, USA
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47
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Abstract
Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression. CGV emerges from both neutral and selective processes, and it may inform about how human populations respond to change. CGV facilitates adaptation in experimental settings, but does it have an important role in the real world? Here, we review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution.
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Affiliation(s)
- Annalise B Paaby
- Department of Biology, and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York 10003, USA
| | - Matthew V Rockman
- Department of Biology, and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York 10003, USA
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48
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Snoek LB, Joeri van der Velde K, Li Y, Jansen RC, Swertz MA, Kammenga JE. Worm variation made accessible: Take your shopping cart to store, link, and investigate! WORM 2014; 3:e28357. [PMID: 24843834 PMCID: PMC4024057 DOI: 10.4161/worm.28357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/17/2014] [Accepted: 02/25/2014] [Indexed: 11/20/2022]
Abstract
In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans.
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Affiliation(s)
- L Basten Snoek
- Laboratory of Nematology; Wageningen University; The Netherlands
| | - K Joeri van der Velde
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands ; Department of Genetics; University of Groningen; University Medical Center Groningen; The Netherlands
| | - Yang Li
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Center; University of Groningen; The Netherlands
| | - Morris A Swertz
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands ; Department of Genetics; University of Groningen; University Medical Center Groningen; The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology; Wageningen University; The Netherlands
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