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Ishita Y, Onodera A, Ekino T, Chihara T, Okumura M. Co-option of an Astacin Metalloprotease Is Associated with an Evolutionarily Novel Feeding Morphology in a Predatory Nematode. Mol Biol Evol 2023; 40:msad266. [PMID: 38105444 PMCID: PMC10753534 DOI: 10.1093/molbev/msad266] [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: 03/28/2023] [Revised: 10/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Animals consume a wide variety of food sources to adapt to different environments. However, the genetic mechanisms underlying the acquisition of evolutionarily novel feeding morphology remain largely unknown. While the nematode Caenorhabditis elegans feeds on bacteria, the satellite species Pristionchus pacificus exhibits predatory feeding behavior toward other nematodes, which is an evolutionarily novel feeding habit. Here, we found that the astacin metalloprotease Ppa-NAS-6 is required for the predatory killing by P. pacificus. Ppa-nas-6 mutants were defective in predation-associated characteristics, specifically the tooth morphogenesis and tooth movement during predation. Comparison of expression patterns and rescue experiments of nas-6 in P. pacificus and C. elegans suggested that alteration of the spatial expression patterns of NAS-6 may be vital for acquiring predation-related traits. Reporter analysis of the Ppa-nas-6 promoter in C. elegans revealed that the alteration in expression patterns was caused by evolutionary changes in cis- and trans-regulatory elements. This study suggests that the co-option of a metalloprotease is involved in an evolutionarily novel feeding morphology.
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Affiliation(s)
- Yuuki Ishita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ageha Onodera
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Taisuke Ekino
- School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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Cao M. CRISPR-Cas9 genome editing in Steinernema entomopathogenic nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.24.568619. [PMID: 38045388 PMCID: PMC10690278 DOI: 10.1101/2023.11.24.568619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Molecular tool development in traditionally non-tractable animals opens new avenues to study gene functions in the relevant ecological context. Entomopathogenic nematodes (EPN) Steinernema and their symbiotic bacteria of Xenorhabdus spp are a valuable experimental system in the laboratory and are applicable in the field to promote agricultural productivity. The infective juvenile (IJ) stage of the nematode packages mutualistic symbiotic bacteria in the intestinal pocket and invades insects that are agricultural pests. The lack of consistent and heritable genetics tools in EPN targeted mutagenesis severely restricted the study of molecular mechanisms underlying both parasitic and mutualistic interactions. Here, I report a protocol for CRISPR-Cas9 based genome-editing that is successful in two EPN species, S. carpocapsae and S. hermaphroditum . I adapted a gonadal microinjection technique in S. carpocapsae , which created on-target modifications of a homologue Sc-dpy-10 (cuticular collagen) by homology-directed repair. A similar delivery approach was used to introduce various alleles in S. hermaphroditum including Sh-dpy-10 and Sh-unc-22 (a muscle gene), resulting in visible and heritable phenotypes of dumpy and twitching, respectively. Using conditionally dominant alleles of Sh-unc-22 as a co-CRISPR marker, I successfully modified a second locus encoding Sh-Daf-22 (a homologue of human sterol carrier protein SCPx), predicted to function as a core enzyme in the biosynthesis of nematode pheromone that is required for IJ development. As a proof of concept, Sh-daf-22 null mutant showed IJ developmental defects in vivo ( in insecta) . This research demonstrates that Steinernema spp are highly tractable for targeted mutagenesis and has great potential in the study of gene functions under controlled laboratory conditions within the relevant context of its ecological niche.
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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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Wighard SS, Athanasouli M, Witte H, Rödelsperger C, Sommer RJ. A New Hope: A Hermaphroditic Nematode Enables Analysis of a Recent Whole Genome Duplication Event. Genome Biol Evol 2022; 14:6868937. [PMID: 36461901 PMCID: PMC9763058 DOI: 10.1093/gbe/evac169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/03/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Whole genome duplication (WGD) is often considered a major driver of evolution that leads to phenotypic novelties. However, the importance of WGD for evolution is still controversial because most documented WGD events occurred anciently and few experimental systems amenable to genetic analysis are available. Here, we report a recent WGD event in the hermaphroditic nematode Allodiplogaster sudhausi and present a comparison with a gonochoristic (male/female) sister species that did not undergo WGD. Self-fertilizing reproduction of A. sudhausi makes it amenable to functional analysis and an ideal system to study WGD events. We document WGD in A. sudhausi through karyotype analysis and whole genome sequencing, the latter of which allowed us to 1) identify functional bias in retention of protein domains and metabolic pathways, 2) show most duplicate genes are under evolutionary constraint, 3) show a link between sequence and expression divergence, and 4) characterize differentially expressed duplicates. We additionally show WGD is associated with increased body size and an abundance of repeat elements (36% of the genome), including a recent expansion of the DNA-hAT/Ac transposon family. Finally, we demonstrate the use of CRISPR/Cas9 to generate mutant knockouts, whereby two WGD-derived duplicate genes display functional redundancy in that they both need to be knocked out to generate a phenotype. Together, we present a novel experimental system that is convenient for examining and characterizing WGD-derived genes both computationally and functionally.
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Affiliation(s)
- Sara S Wighard
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Marina Athanasouli
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
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Ogino H, Kamei Y, Hayashi T, Sakamoto J, Suzuki M, Igawa T. Invention sharing is the mother of developmental biology. Dev Growth Differ 2021; 63:458. [PMID: 34967943 DOI: 10.1111/dgd.12763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hajime Ogino
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yasuhiro Kamei
- Spectrography and Bioimaging Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Joe Sakamoto
- Spectrography and Bioimaging Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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