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Ma J, Zhou W, Shao W, Li Y. Efficient Knock-in by CRISPR/Cas9-mediated homology-directed repair in Caenorhabditis briggsae. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001203. [PMID: 39055349 PMCID: PMC11270111 DOI: 10.17912/micropub.biology.001203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/14/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
The CRISPR/Cas9 technology opens new avenues for detailed genetic exploration and comparative genomics. However, the current application of CRISPR/Cas9 in C. briggsae especially for homology-directed repair (HDR) knock-in (KI) still encounter significant challenges. In this study, we demonstrate that employing high concentration HDR donor vectors significantly improves KI efficiency in C. briggsae .
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Affiliation(s)
- Jiaonv Ma
- College of Life Science, Capital Normal University, Beijing, Beijing, China
| | - Wangyan Zhou
- College of Life Science, Capital Normal University, Beijing, Beijing, China
| | - Wenhua Shao
- College of Life Science, Capital Normal University, Beijing, Beijing, China
| | - Yongbin Li
- College of Life Science, Capital Normal University, Beijing, Beijing, China
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Alkan C, Brésard G, Frézal L, Richaud A, Ruaud A, Zhang G, Félix MA. Natural variation in infection specificity of Caenorhabditis briggsae isolates by two RNA viruses. PLoS Pathog 2024; 20:e1012259. [PMID: 38861582 PMCID: PMC11195985 DOI: 10.1371/journal.ppat.1012259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/24/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Antagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematode C. elegans. In contrast, several related RNA viruses infect its congener C. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the host's intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-origin C. briggsae strains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, some C. briggsae strains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains' geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection.
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Affiliation(s)
- Cigdem Alkan
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gautier Brésard
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Lise Frézal
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques Paris, Paris, France
| | - Aurélien Richaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Albane Ruaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gaotian Zhang
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Marie-Anne Félix
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
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Gang SS, Lažetić V. Microsporidia: Pervasive natural pathogens of Caenorhabditis elegans and related nematodes. J Eukaryot Microbiol 2024:e13027. [PMID: 38702921 DOI: 10.1111/jeu.13027] [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: 01/15/2024] [Accepted: 02/02/2024] [Indexed: 05/06/2024]
Abstract
The nematode Caenorhabditis elegans is an invaluable host model for studying infections caused by various pathogens, including microsporidia. Microsporidia represent the first natural pathogens identified in C. elegans, revealing the previously unknown Nematocida genus of microsporidia. Following this discovery, the utilization of nematodes as a model host has rapidly expanded our understanding of microsporidia biology and has provided key insights into the cell and molecular mechanisms of antimicrosporidia defenses. Here, we first review the isolation history, morphological characteristics, life cycles, tissue tropism, genetics, and host immune responses for the four most well-characterized Nematocida species that infect C. elegans. We then highlight additional examples of microsporidia that infect related terrestrial and aquatic nematodes, including parasitic nematodes. To conclude, we assess exciting potential applications of the nematode-microsporidia system while addressing the technical advances necessary to facilitate future growth in this field.
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Affiliation(s)
- Spencer S Gang
- Molecular Biology Department, Colorado College, Colorado Springs, Colorado, USA
| | - Vladimir Lažetić
- Department of Biological Sciences, Columbian College of Arts & Sciences, The George Washington University, Washington, District of Columbia, USA
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Hellekes V, Claus D, Seiler J, Illner F, Schiffer PH, Kroiher M. CRISPR/Cas9 mediated gene editing in non-model nematode Panagrolaimus sp. PS1159. Front Genome Ed 2023; 5:1078359. [PMID: 36818277 PMCID: PMC9935820 DOI: 10.3389/fgeed.2023.1078359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The phylum Nematoda harbors a huge diversity of species in a broad range of ecosystems and habitats. Nematodes share a largely conserved Bauplan but major differences have been found in early developmental processes. The development of the nematode model organism Caenorhabditis elegans has been studied in great detail for decades. These efforts have provided the community with a large number of protocols and methods. Unfortunately, many of these tools are not easily applicable in non-Caenorhabditis nematodes. In recent years it has become clear that many crucial genes in the C. elegans developmental toolkit are absent in other nematode species. It is thus necessary to study the developmental program of other nematode species in detail to understand evolutionary conservation and novelty in the phylum. Panagrolaimus sp. PS1159 is a non-parasitic nematode exhibiting parthenogenetic reproduction and we are establishing the species to comparatively study evolution, biodiversity, and alternative reproduction and survival strategies. Here, we demonstrate the first successful application of the CRISPR/Cas9 system for genome editing in Panagrolaimus sp. PS1159 and the closely related hermaphroditic species Propanagrolaimus sp. JU765 applying the non-homologous end joining and the homology-directed repair (HDR) mechanisms. Using microinjections and modifying published protocols from C. elegans and P. pacificus we induced mutations in the orthologue of unc-22. This resulted in a visible uncoordinated twitching phenotype. We also compared the HDR efficiency following the delivery of different single-stranded oligodeoxynucleotides (ssODNs). Our work will expand the applicability for a wide range of non-model nematodes from across the tree and facilitate functional analysis into the evolution of parthenogenesis, changes in the developmental program of Nematoda, and cryptobiosis.
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Affiliation(s)
- Viktoria Hellekes
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany,Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany,*Correspondence: Viktoria Hellekes,
| | - Denise Claus
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Johanna Seiler
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Felix Illner
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Philipp H. Schiffer
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Michael Kroiher
- Institute for Zoology, University of Cologne, Cologne, NRW, Germany
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Kim HM, Hong Y, Chen J. A Decade of CRISPR-Cas Gnome Editing in C. elegans. Int J Mol Sci 2022; 23:ijms232415863. [PMID: 36555505 PMCID: PMC9781986 DOI: 10.3390/ijms232415863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas allows us to introduce desired genome editing, including mutations, epitopes, and deletions, with unprecedented efficiency. The development of CRISPR-Cas has progressed to such an extent that it is now applicable in various fields, with the help of model organisms. C. elegans is one of the pioneering animals in which numerous CRISPR-Cas strategies have been rapidly established over the past decade. Ironically, the emergence of numerous methods makes the choice of the correct method difficult. Choosing an appropriate selection or screening approach is the first step in planning a genome modification. This report summarizes the key features and applications of CRISPR-Cas methods using C. elegans, illustrating key strategies. Our overview of significant advances in CRISPR-Cas will help readers understand the current advances in genome editing and navigate various methods of CRISPR-Cas genome editing.
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Linc00261 Inhibited High-Grade Serous Ovarian Cancer Progression through miR-552-ATG10-EMT Axis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9450353. [PMID: 35465017 PMCID: PMC9019445 DOI: 10.1155/2022/9450353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 12/05/2022]
Abstract
In recent years, long non-coding RNAs (lncRNAs) play an important role in a multitude of pathways across species; however, their functions are still unknown. In this study, we demonstrate that Linc00261 is downregulation in high-grade serous ovarian cancer (HGSOC) and can inhibit cell proliferation and migration of high-grade serous ovarian cancer cells. We further validate the targeting interactions among Linc00261, miR-552, and ATG10. Interestingly, they all play important roles for regulating epithelial-mesenchymal transition (EMT) progression. Collectively, these findings suggest that Linc00261, a mediator of EMT progression, can target oncogenic miR-552, elevating ATG10 expression, to prevent high-grade serous ovarian cancer tumorigenesis and may serve as a potential novel therapeutic target.
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Cohen SM, Wrobel CJJ, Prakash SJ, Schroeder FC, Sternberg PW. Formation and function of dauer ascarosides in the nematodes Caenorhabditis briggsae and Caenorhabditis elegans. G3 GENES|GENOMES|GENETICS 2022; 12:6517505. [PMID: 35094091 PMCID: PMC8895998 DOI: 10.1093/g3journal/jkac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/22/2021] [Indexed: 11/12/2022]
Abstract
Abstract
The biosynthetic pathways and functions of ascaroside signaling molecules in the nematode Caenorhabditis elegans have been studied to better understand complex, integrative developmental decision-making. Although it is known that ascarosides play multiple roles in the development and behavior of nematode species other than C. elegans, these parallel pheromone systems have not been well-studied. Here, we show that ascarosides in the nematode Caenorhabditis briggsae are biosynthesized in the same manner as C. elegans and act to induce the alternative developmental pathway that generates the stress-resistant dauer lifestage. We show that ascr#2 is the primary component of crude dauer pheromone in C. briggsae; in contrast, C. elegans dauer pheromone relies on a combination of ascr#2, ascr#3, and several other components. We further demonstrate that Cbr-daf-22, like its C. elegans ortholog Cel-daf-22, is necessary to produce short-chain ascarosides. Moreover, Cbr-daf-22 and Cel-daf-22 mutants produce an ascaroside-independent metabolite that acts antagonistically to crude dauer pheromone and inhibits dauer formation.
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Affiliation(s)
- Sarah M Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sharan J Prakash
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Wang W, Flury AG, Garrison JL, Brem RB. Cold Survival and Its Molecular Mechanisms in a Locally Adapted Nematode Population. Genome Biol Evol 2021; 13:evab188. [PMID: 34383891 PMCID: PMC8449824 DOI: 10.1093/gbe/evab188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 11/25/2022] Open
Abstract
Since Darwin, evolutionary biologists have sought to understand the drivers and mechanisms of natural trait diversity. The field advances toward this goal with the discovery of phenotypes that vary in the wild, their relationship to ecology, and their underlying genes. Here, we established resistance to extreme low temperature in the free-living nematode Caenorhabditis briggsae as an ecological and evolutionary model system. We found that C. briggsae strains of temperate origin were strikingly more cold-resistant than those isolated from tropical localities. Transcriptional profiling revealed expression patterns unique to the resistant temperate ecotype, including dozens of genes expressed at high levels even after multiple days of cold-induced physiological slowdown. Mutational analysis validated a role in cold resistance for seven such genes. These findings highlight a candidate case of robust, genetically complex adaptation in an emerging model nematode, and shed light on the mechanisms at play.
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Affiliation(s)
- Wenke Wang
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
| | - Anna G Flury
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
| | - Jennifer L Garrison
- Buck Institute for Research on Aging, Novato, California, USA
- Leonard Davis School of Gerontology, University of Southern California, USA
- Department of Cellular and Molecular Pharmacology, UC San Francisco, USA
- Global Consortium for Reproductive Longevity & Equality, Novato, California, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
- Leonard Davis School of Gerontology, University of Southern California, USA
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