1
|
Sundaram MV, Pujol N. The Caenorhabditis elegans cuticle and precuticle: a model for studying dynamic apical extracellular matrices in vivo. Genetics 2024; 227:iyae072. [PMID: 38995735 PMCID: PMC11304992 DOI: 10.1093/genetics/iyae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/25/2024] [Indexed: 07/14/2024] Open
Abstract
Apical extracellular matrices (aECMs) coat the exposed surfaces of animal bodies to shape tissues, influence social interactions, and protect against pathogens and other environmental challenges. In the nematode Caenorhabditis elegans, collagenous cuticle and zona pellucida protein-rich precuticle aECMs alternately coat external epithelia across the molt cycle and play many important roles in the worm's development, behavior, and physiology. Both these types of aECMs contain many matrix proteins related to those in vertebrates, as well as some that are nematode-specific. Extensive differences observed among tissues and life stages demonstrate that aECMs are a major feature of epithelial cell identity. In addition to forming discrete layers, some cuticle components assemble into complex substructures such as ridges, furrows, and nanoscale pillars. The epidermis and cuticle are mechanically linked, allowing the epidermis to sense cuticle damage and induce protective innate immune and stress responses. The C. elegans model, with its optical transparency, facilitates the study of aECM cell biology and structure/function relationships and all the myriad ways by which aECM can influence an organism.
Collapse
Affiliation(s)
- Meera V Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nathalie Pujol
- Aix Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, 13009 Marseille, France
| |
Collapse
|
2
|
Emser J, Wernet N, Hetzer B, Wohlmann E, Fischer R. The cysteine-rich virulence factor NipA of Arthrobotrys flagrans interferes with cuticle integrity of Caenorhabditis elegans. Nat Commun 2024; 15:5795. [PMID: 38987250 PMCID: PMC11237121 DOI: 10.1038/s41467-024-50096-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 06/27/2024] [Indexed: 07/12/2024] Open
Abstract
Animals protect themself from microbial attacks by robust skins or a cuticle as in Caenorhabditis elegans. Nematode-trapping fungi, like Arthrobotrys flagrans, overcome the cuticle barrier and colonize the nematode body. While lytic enzymes are important for infection, small-secreted proteins (SSPs) without enzymatic activity, emerge as crucial virulence factors. Here, we characterized NipA (nematode induced protein) which A. flagrans secretes at the penetration site. In the absence of NipA, A. flagrans required more time to penetrate C. elegans. Heterologous expression of the fungal protein in the epidermis of C. elegans led to blister formation. NipA contains 13 cysteines, 12 of which are likely to form disulfide bridges, and the remaining cysteine was crucial for blister formation. We hypothesize that NipA interferes with cuticle integrity to facilitate fungal entry. Genome-wide expression analyses of C. elegans expressing NipA revealed mis-regulation of genes associated with extracellular matrix (ECM) maintenance and innate immunity.
Collapse
Affiliation(s)
- Jennifer Emser
- Institute for Applied Biosciences. Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Nicole Wernet
- Institute for Applied Biosciences. Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Birgit Hetzer
- Max Rubner-Institut (MRI) - Federal Research Institute of Nutrition and Food, Haid-und-Neu-Strasse 9, Karlsruhe, 76131, Germany
| | - Elke Wohlmann
- Institute for Applied Biosciences. Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Reinhard Fischer
- Institute for Applied Biosciences. Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany.
| |
Collapse
|
3
|
Sparling AC, King DE, Meyer JN. rol-6 and dpy-10C. elegans mutants have normal mitochondrial function after normalizing to delayed development. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000798. [PMID: 37215639 PMCID: PMC10193146 DOI: 10.17912/micropub.biology.000798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023]
Abstract
Collagen mutations are commonly used in the creation of Caenorhabditis elegans transgenic strains, but their secondary effects are not fully characterized . We compared the mitochondrial function of N2, dpy-10, rol-6, and PE255 C. elegans . N2 worms exhibited ~2-fold greater volume, mitochondrial DNA copy number, and nuclear DNA copy number than collagen mutants (p<0.05). Whole-worm respirometry and ATP levels were higher in N2 worms, but differences in respirometry largely disappeared after normalization to mitochondrial DNA copy number. This data suggests that rol-6 and dpy-10 mutants are developmentally delayed but have comparable mitochondrial function to N2 worms once the data is normalized to developmental stage.
Collapse
Affiliation(s)
| | - Dillon E. King
- Nicholas School of Environment, Duke University, Durham NC
| | - Joel N. Meyer
- Nicholas School of Environment, Duke University, Durham NC
| |
Collapse
|
4
|
Malaiwong N, Porta-de-la-Riva M, Krieg M. FLInt: single shot safe harbor transgene integration via Fluorescent Landmark Interference. G3 (BETHESDA, MD.) 2023; 13:jkad041. [PMID: 36805659 PMCID: PMC10151404 DOI: 10.1093/g3journal/jkad041] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023]
Abstract
The stable incorporation of transgenes and recombinant DNA material into the host genome is a bottleneck in many bioengineering applications. Due to the low efficiency, identifying the transgenic animals is often a needle in the haystack. Thus, optimal conditions require efficient screening procedures, but also known and safe landing sites that do not interfere with host expression, low input material and strong expression from the new locus. Here, we leverage an existing library of ≈300 different loci coding for fluorescent markers that are distributed over all 6 chromosomes in Caenorhabditis elegans as safe harbors for versatile transgene integration sites using CRISPR/Cas9. We demonstrated that a single crRNA was sufficient for cleavage of the target region and integration of the transgene of interest, which can be easily followed by loss of the fluorescent marker. The same loci can also be used for extrachromosomal landing sites and as co-CRISPR markers without affecting body morphology or animal behavior. Thus, our method overcomes the uncertainty of transgene location during random mutagenesis, facilitates easy screening through fluorescence interference and can be used as co-CRISPR markers without further influence in phenotypes.
Collapse
Affiliation(s)
| | | | - Michael Krieg
- Corresponding author: Institut de Ciències Fotòniques (ICFO), 08860 Castelldefels, Spain.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Li Zheng S, Adams JG, Chisholm AD. Form and function of the apical extracellular matrix: new insights from Caenorhabditis elegans, Drosophila melanogaster, and the vertebrate inner ear. Fac Rev 2020; 9:27. [PMID: 33659959 PMCID: PMC7886070 DOI: 10.12703/r/9-27] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Apical extracellular matrices (aECMs) are the extracellular layers on the apical sides of epithelia. aECMs form the outer layer of the skin in most animals and line the luminal surface of internal tubular epithelia. Compared to the more conserved basal ECMs (basement membranes), aECMs are highly diverse between tissues and between organisms and have been more challenging to understand at mechanistic levels. Studies in several genetic model organisms are revealing new insights into aECM composition, biogenesis, and function and have begun to illuminate common principles and themes of aECM organization. There is emerging evidence that, in addition to mechanical or structural roles, aECMs can participate in reciprocal signaling with associated epithelia and other cell types. Studies are also revealing mechanisms underlying the intricate nanopatterns exhibited by many aECMs. In this review, we highlight recent findings from well-studied model systems, including the external cuticle and ductal aECMs of Caenorhabditis elegans, Drosophila melanogaster, and other insects and the internal aECMs of the vertebrate inner ear.
Collapse
Affiliation(s)
- Sherry Li Zheng
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Gotenstein Adams
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrew D Chisholm
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
8
|
Cohen JD, Sundaram MV. C. elegans Apical Extracellular Matrices Shape Epithelia. J Dev Biol 2020; 8:E23. [PMID: 33036165 PMCID: PMC7712855 DOI: 10.3390/jdb8040023] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Apical extracellular matrices (aECMs) coat exposed surfaces of epithelia to shape developing tissues and protect them from environmental insults. Despite their widespread importance for human health, aECMs are poorly understood compared to basal and stromal ECMs. The nematode Caenorhabditis elegans contains a variety of distinct aECMs, some of which share many of the same types of components (lipids, lipoproteins, collagens, zona pellucida domain proteins, chondroitin glycosaminoglycans and proteoglycans) with mammalian aECMs. These aECMs include the eggshell, a glycocalyx-like pre-cuticle, both collagenous and chitin-based cuticles, and other understudied aECMs of internal epithelia. C. elegans allows rapid genetic manipulations and live imaging of fluorescently-tagged aECM components, and is therefore providing new insights into aECM structure, trafficking, assembly, and functions in tissue shaping.
Collapse
Affiliation(s)
| | - Meera V. Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine 415 Curie Blvd, Philadelphia, PA 19104-6145, USA;
| |
Collapse
|