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Korhonen PK, Wang T, Young ND, Byrne JJ, Campos TL, Chang BC, Taki AC, Gasser RB. Analysis of Haemonchus embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates. Comput Struct Biotechnol J 2024; 23:1026-1035. [PMID: 38435301 PMCID: PMC10907403 DOI: 10.1016/j.csbj.2024.01.008] [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: 10/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms. Here, we created the first single cell atlas for an early developmental stage of Haemonchus contortus - a highly pathogenic, C. elegans-related parasitic nematode. We obtained and curated RNA sequence (snRNA-seq) data from single nuclei from embryonating eggs of H. contortus (150,000 droplets), and selected high-quality transcriptomic data for > 14,000 single nuclei for analysis, and identified 19 distinct clusters of cells. Guided by comparative analyses with C. elegans, we were able to reproducibly assign seven cell clusters to body wall muscle, hypodermis, neuronal, intestinal or seam cells, and identified eight genes that were transcribed in all cell clusters/types, three of which were inferred to be essential in H. contortus. Two of these genes (i.e. Hc-eef-1A and Hc-eef1G), coding for eukaryotic elongation factors (called Hc-eEF1A and Hc-eEF1G), were also demonstrated to be transcribed and expressed in all key developmental stages of H. contortus. Together with these findings, sequence- and structure-based comparative analyses indicated the potential of Hc-eEF1A and/or Hc-eEF1G as intervention targets within the protein biosynthesis machinery of H. contortus. Future work will focus on single cell studies of all key developmental stages and tissues of H. contortus, and on evaluating the suitability of the two elongation factor proteins as drug targets in H. contortus and related nematodes, with a view to finding new nematocidal drug candidates.
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Affiliation(s)
- Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
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Nikolaidou C, Mola M, Papakostas S, Aschonitis VG, Monokrousos N, Kougias PG. The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-32850-9. [PMID: 38517633 DOI: 10.1007/s11356-024-32850-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024]
Abstract
Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.
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Affiliation(s)
- Charitini Nikolaidou
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece
- University Center of International Programmes of Studies, International Hellenic University, 57001, Thessaloniki, Greece
| | - Magkdi Mola
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece
- University Center of International Programmes of Studies, International Hellenic University, 57001, Thessaloniki, Greece
| | - Spiros Papakostas
- Department of Science and Technology, International Hellenic University, 57001, Thessaloniki, Greece
| | - Vassilis G Aschonitis
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece
| | - Nikolaos Monokrousos
- University Center of International Programmes of Studies, International Hellenic University, 57001, Thessaloniki, Greece
| | - Panagiotis G Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organization Dimitra, 57001, Thessaloniki, Greece.
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3
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Jung J, Loschko T, Reich S, Rassoul-Agha M, Werner MS. Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions. Proc Biol Sci 2024; 291:20232653. [PMID: 38471558 PMCID: PMC10932707 DOI: 10.1098/rspb.2023.2653] [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: 11/28/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.
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Affiliation(s)
- Julie Jung
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tobias Loschko
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
- Max Planck Institute for Biology, Tübingen, Germany
| | - Shelley Reich
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Maxim Rassoul-Agha
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Michael S. Werner
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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4
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Mo YX, Kan YZ, Jia LM, Cao XT, Sikandar A, Wu HY. Characterization and Effect of a Nematophagous Fungus Talaromyces cystophila sp. nov. for the Biological Control of Corn Cyst Nematode. PHYTOPATHOLOGY 2024; 114:618-629. [PMID: 37889191 DOI: 10.1094/phyto-02-23-0045-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The dynamic of plant-parasitic nematode populations in soil is closely related to soil microorganisms. Fungi from Heterodera zeae cysts were isolated to explore the phenomenon of decline in the H. zeae population in the soil. Phylogenetic study of partial ITS, BenA, CaM, and RPB2 gene sequences, in addition to morphological investigations, was utilized to identify a nematode-destroying fungus. The nematicidal activity of a novel strain GX1 against H. zeae was assessed in vitro and in the greenhouse. Our findings revealed that strain GX1 is a new species of Talaromyces, named Talaromyces cystophila. It has a strong parasitic and lethal effect on H. zeae cysts, with 91.11% parasitism on cysts at 3 days after treatment. The contents of second-stage juveniles (J2s) and eggs inside the cysts were degraded and formed dense vacuoles, and the damaged eggs could not hatch normally. The spore suspension exhibited high nematophagous activity against nematodes, and fermentation filtrate exhibited marked inhibition of egg hatching and nematicidal activities on J2s. The hatching inhibition rates of eggs exposed to 1 × 108 CFU/ml spore suspensions or 20% 1-week fermentation filtrate (1-WF) for 15 days were 98.56 and 100%, respectively. The mortality of J2s exposed to 1 × 108 CFU/ml spore suspension reached 100% at 24 h; exposure to 50% 2-WF was 98.65 and 100% at 24 and 48 h, respectively. Greenhouse experiments revealed that the spore suspension and fermentation broth considerably decreased H. zeae reproduction by 56.17 to 78.76%. T. cystophila is a potential biocontrol strain with nematophagous and nematicidal activity that deserves attention and application.
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Affiliation(s)
- Yi Xue Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Yuan Zi Kan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Lu Ming Jia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Xiao Tian Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Aatika Sikandar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hai Yan Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China
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5
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Lin CJ, Siddique S. Parasitic nematodes: dietary habits and their implications. Trends Parasitol 2024; 40:230-240. [PMID: 38262837 DOI: 10.1016/j.pt.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Nematodes, a diverse group of roundworms, exhibit a wide range of dietary habits, including parasitism of animals and plants. These parasites cause substantial economic losses in agriculture and pose significant health challenges to humans and animals. This review explores the unique adaptations of parasitic nematodes, emphasizing their nutritional requirements and metabolic dependencies. Recent research has identified cross-kingdom compartmentalization of vitamin B5 biosynthesis in some parasitic nematodes, shedding light on coevolutionary dynamics and potential targets for control strategies. Several open questions remain regarding the complexity of nematode nutrition, host manipulation, evolutionary adaptations, and the influence of environmental factors on their metabolic processes. Understanding these aspects offers promising avenues for targeted interventions to manage and control these economically and medically important parasites.
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Affiliation(s)
- Ching-Jung Lin
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA.
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6
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Trejo‐Meléndez VJ, Ibarra‐Rendón J, Contreras‐Garduño J. The evolution of entomopathogeny in nematodes. Ecol Evol 2024; 14:e10966. [PMID: 38352205 PMCID: PMC10862191 DOI: 10.1002/ece3.10966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding how parasites evolved is crucial to understand the host and parasite interaction. The evolution of entomopathogenesis in rhabditid nematodes has traditionally been thought to have occurred twice within the phylum Nematoda: in Steinernematidae and Heterorhabditidae families, which are associated with the entomopathogenic bacteria Xenorhabdus and Photorhabdus, respectively. However, nematodes from other families that are associated with entomopathogenic bacteria have not been considered to meet the criteria for "entomopathogenic nematodes." The evolution of parasitism in nematodes suggests that ecological and evolutionary properties shared by families in the order Rhabditida favor the convergent evolution of the entomopathogenic trait in lineages with diverse lifestyles, such as saprotrophs, phoretic, and necromenic nematodes. For this reason, this paper proposes expanding the term "entomopathogenic nematode" considering the diverse modes of this attribute within Rhabditida. Despite studies are required to test the authenticity of the entomopathogenic trait in the reported species, they are valuable links that represent the early stages of specialized lineages to entomopathogenic lifestyle. An ecological and evolutionary exploration of these nematodes has the potential to deepen our comprehension of the evolution of entomopathogenesis as a convergent trait spanning across the Nematoda.
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Affiliation(s)
- V. J. Trejo‐Meléndez
- Edificio de Investigación I, ENES, Unidad Morelia, UNAMMoreliaMichoacánMexico
- Posgrado en Ciencias Biológicas, ENES, Unidad Morelia, UNAMMoreliaMichoacánMexico
| | - J. Ibarra‐Rendón
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV) – IrapuatoIrapuatoGuanajuatoMexico
| | - J. Contreras‐Garduño
- Edificio de Investigación I, ENES, Unidad Morelia, UNAMMoreliaMichoacánMexico
- Institute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
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7
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Ko I, Kranse OP, Senatori B, Eves-van den Akker S. A Critical Appraisal of DNA Transfer from Plants to Parasitic Cyst Nematodes. Mol Biol Evol 2024; 41:msae030. [PMID: 38366574 PMCID: PMC10899095 DOI: 10.1093/molbev/msae030] [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: 05/04/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 02/18/2024] Open
Abstract
Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that horizontal gene transfer-the natural acquisition of foreign genes in parasitic nematodes-contributes to parasitism. However, an apparent paradox has emerged from horizontal gene transfer analyses: On the one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only transient interactions with nematodes as far as we know, dominate the list of putative donors, while on the other hand, considerably more closely related organisms (i.e. the host plant), with similar genetic structure (i.e. introns) and documented long-term associations with nematodes, are rare among the list of putative donors. Given that these nematodes ingest cytoplasm from a living plant cell for several weeks, there seems to be a conspicuous absence of plant-derived cases. Here, we used comparative genomic approaches to evaluate possible plant-derived horizontal gene transfer events in plant parasitic nematodes. Our evidence supports a cautionary message for plant-derived horizontal gene transfer cases in the sugar beet cyst nematode, Heterodera schachtii. We propose a 4-step model for horizontal gene transfer from plant to parasite in order to evaluate why the absence of plant-derived horizontal gene transfer cases is observed. We find that the plant genome is mobilized by the nematode during infection, but that uptake of the said "mobilome" is the first major barrier to horizontal gene transfer from host to nematode. These results provide new insight into our understanding of the prevalence/role of nucleic acid exchange in the arms race between plants and plant parasites.
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Affiliation(s)
- Itsuhiro Ko
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
- Present address: Department of Plant Pathology, Washington State University, Pullman 99163, USA
| | - Olaf Prosper Kranse
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
| | - Beatrice Senatori
- Department of Plant Sciences, The Crop Science Centre, University of Cambridge, Cambridge CB2 3EA, UK
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Seimandi GM, Imhoff SDC, Derita MG. Bioactivity of Raphanus Species against Agricultural Phytopathogens and its Role in Soil Remediation: A Review. Comb Chem High Throughput Screen 2024; 27:516-544. [PMID: 37415376 DOI: 10.2174/1386207326666230706123818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Phytopathogens and weeds represent around 20-40% of global agricultural productivity losses. Synthetic pesticide products are the most used to combat these pests, but it reiterates that their use has caused tremendous pressure on ecosystems' self-cleansing capacity and resistance development by pathogens to synthetic fungicides. In the last decades, researchers have demonstrated the vast biological properties of plants against pathogens and diseases. Raphanus species (Brassicaceae) possesses antimicrobial, antioxidant, anti-inflammatory, anticancer, hepatoprotective, antidiabetic, insecticidal, nematicidal, allelopathic, and phytoremediators properties. These are due to the presence of structurally diverse bioactive compounds, such as flavonoids and glucosinolates. In this review, we have provided an update on the biological properties of two Raphanus species (R. sativus and R. raphanistrum), detailing the type of natural product (extract or isolated compound), the bioassays displayed, and the results obtained for the main bioactivities of this genus cited in the literature during the last 30 years. Moreover, preliminary studies on phytopathogenic activities performed in our laboratory have also been depicted. We conclude that Raphanus species could be a source of natural bioactive molecules to treat phytopathogens and weeds that affect crops and remediate contaminated soils.
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Affiliation(s)
- Gisela Marisol Seimandi
- ICiAgro Litoral (Universidad Nacional del Litoral-CONICET), Esperanza, Santa Fe, 3080HOF, Argentina
| | - Silvia Del Carmen Imhoff
- ICiAgro Litoral (Universidad Nacional del Litoral-CONICET), Esperanza, Santa Fe, 3080HOF, Argentina
| | - Marcos Gabriel Derita
- ICiAgro Litoral (Universidad Nacional del Litoral-CONICET), Esperanza, Santa Fe, 3080HOF, Argentina
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha, 531, S2002LRK, Rosario, Argentina
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9
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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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10
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Wang C, Ronan EA, Kim SK, Kitsopoulos P, Iliff AJ, Grosh K, Kim GH, Liu J, Xu XZS. Sensing of sound pressure gradients by C. elegans drives phonotaxis behavior. Curr Biol 2023; 33:3985-3991.e4. [PMID: 37643623 PMCID: PMC10575617 DOI: 10.1016/j.cub.2023.08.005] [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: 04/03/2023] [Revised: 07/06/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
Despite lacking ears, the nematode C. elegans senses airborne sound and engages in phonotaxis behavior, enabling it to locate and avoid sound sources.1 How worms sense sound, however, is not well understood. Here, we report an interesting observation that worms respond only to sounds emitted by small but not large speakers, indicating that they preferentially respond to localized sound sources. Notably, sounds emitted by small speakers form a sharp sound pressure gradient across the worm body, while sounds from large speakers do not, suggesting that worms sense sound pressure gradients rather than absolute sound pressure. Analysis of phonotaxis behavior, sound-evoked skin vibration, and sound-sensitive neuron activities further support this model. We suggest that the ability to sense sound pressure gradients provides a potential mechanism for worms to distinguish sounds generated by their predators, which are typically small animals, from those produced by large animals or background noise. As vertebrate cochlea and some insect ears can also detect sound pressure gradients, our results reveal that sensing of sound pressure gradients may represent a common mechanism in auditory sensation across animal phyla. VIDEO ABSTRACT.
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Affiliation(s)
- Can Wang
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth A Ronan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shin-Kwan Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan, South Korea
| | - Panagiota Kitsopoulos
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adam J Iliff
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karl Grosh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gun-Ho Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan, South Korea
| | - Jianfeng Liu
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - X Z Shawn Xu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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Freires IA, Morelo DFC, Soares LFF, Costa IS, de Araújo LP, Breseghello I, Abdalla HB, Lazarini JG, Rosalen PL, Pigossi SC, Franchin M. Progress and promise of alternative animal and non-animal methods in biomedical research. Arch Toxicol 2023; 97:2329-2342. [PMID: 37394624 DOI: 10.1007/s00204-023-03532-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/04/2023]
Abstract
Cell culture and invertebrate animal models reflect a significant evolution in scientific research by providing reliable evidence on the physiopathology of diseases, screening for new drugs, and toxicological tests while reducing the need for mammals. In this review, we discuss the progress and promise of alternative animal and non-animal methods in biomedical research, with a special focus on drug toxicity.
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Affiliation(s)
- Irlan Almeida Freires
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil.
| | - David Fernando Colon Morelo
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | | | | | | | - Henrique Ballassini Abdalla
- Laboratory of Neuroimmune Interface of Pain Research, São Leopoldo Mandic Institute and Research Center, Campinas, SP, Brazil
| | - Josy Goldoni Lazarini
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Pedro Luiz Rosalen
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
- Graduate Program in Biological Sciences, Federal University of Alfenas, Alfenas, Brazil
| | | | - Marcelo Franchin
- School of Dentistry, Federal University of Alfenas, Alfenas, Brazil
- Bioactivity and Applications Lab, Department of Biological Sciences, Faculty of Science and Engineering, School of Natural Sciences, University of Limerick, Limerick, Ireland
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12
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Anthony MA, Bender SF, van der Heijden MGA. Enumerating soil biodiversity. Proc Natl Acad Sci U S A 2023; 120:e2304663120. [PMID: 37549278 PMCID: PMC10437432 DOI: 10.1073/pnas.2304663120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/02/2023] [Indexed: 08/09/2023] Open
Abstract
Soil is an immense habitat for diverse organisms across the tree of life, but just how many organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity consider only certain types of organisms (e.g., animals) or report values for diverse groups without partitioning species that live in soil versus other habitats. Here, we reviewed the biodiversity literature to show that soil is likely home to 59 ± 15% of the species on Earth. We therefore estimate an approximately two times greater soil biodiversity than previous estimates, and we include representatives from the simplest (microbial) to most complex (mammals) organisms. Enchytraeidae have the greatest percentage of species in soil (98.6%), followed by fungi (90%), Plantae (85.5%), and Isoptera (84.2%). Our results demonstrate that soil is the most biodiverse singular habitat. By using this estimate of soil biodiversity, we can more accurately and quantitatively advocate for soil organismal conservation and restoration as a central goal of the Anthropocene.
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Affiliation(s)
- Mark A. Anthony
- Plant-Soil Interactions Unit, Research Division Agroecology and Environment, Agroscope, Zürich8046, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Forest Dynamics Research Unit, Birmensdorf8903, Switzerland
| | - S. Franz Bender
- Plant-Soil Interactions Unit, Research Division Agroecology and Environment, Agroscope, Zürich8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich8008, Switzerland
| | - Marcel G. A. van der Heijden
- Plant-Soil Interactions Unit, Research Division Agroecology and Environment, Agroscope, Zürich8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich8008, Switzerland
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13
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Yang Y, Zhou J, Wu F, Tong D, Chen X, Jiang S, Duan Y, Yao C, Wang T, Du A, Gasser RB, Ma G. Haem transporter HRG-1 is essential in the barber's pole worm and an intervention target candidate. PLoS Pathog 2023; 19:e1011129. [PMID: 36716341 PMCID: PMC9910794 DOI: 10.1371/journal.ppat.1011129] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/09/2023] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
Parasitic roundworms (nematodes) have lost genes involved in the de novo biosynthesis of haem, but have evolved the capacity to acquire and utilise exogenous haem from host animals. However, very little is known about the processes or mechanisms underlying haem acquisition and utilisation in parasites. Here, we reveal that HRG-1 is a conserved and unique haem transporter in a broad range of parasitic nematodes of socioeconomic importance, which enables haem uptake via intestinal cells, facilitates cellular haem utilisation through the endo-lysosomal system, and exhibits a conspicuous distribution at the basal laminae covering the alimentary tract, muscles and gonads. The broader tissue expression pattern of HRG-1 in Haemonchus contortus (barber's pole worm) compared with its orthologues in the free-living nematode Caenorhabditis elegans indicates critical involvement of this unique haem transporter in haem homeostasis in tissues and organs of the parasitic nematode. RNAi-mediated gene knockdown of hrg-1 resulted in sick and lethal phenotypes of infective larvae of H. contortus, which could only be rescued by supplementation of exogenous haem in the early developmental stage. Notably, the RNAi-treated infective larvae could not establish infection or survive in the mammalian host, suggesting an indispensable role of this haem transporter in the survival of this parasite. This study provides new insights into the haem biology of a parasitic nematode, demonstrates that haem acquisition by HRG-1 is essential for H. contortus survival and infection, and suggests that HRG-1 could be an intervention target candidate in a range of parasitic nematodes.
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Affiliation(s)
- Yi Yang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingru Zhou
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fei Wu
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Danni Tong
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xueqiu Chen
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shengjun Jiang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Duan
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Aifang Du
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail: (AD); (RBG); (GM)
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AD); (RBG); (GM)
| | - Guangxu Ma
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AD); (RBG); (GM)
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14
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Ceron-Noriega A, Almeida MV, Levin M, Butter F. Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis. Genome Res 2023; 33:112-128. [PMID: 36653121 PMCID: PMC9977148 DOI: 10.1101/gr.277070.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/18/2022] [Indexed: 01/19/2023]
Abstract
Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to ∼650-750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry-based proteomics and machine-learning quality control in an approach called proteotranscriptomics, we improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Caenorhabditis elegans Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.
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Affiliation(s)
| | | | - Michal Levin
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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15
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Samita, Utreja D, Dhillon NK. An Efficacious Protocol for the Reduction of Benzothiazole Using Mg/MeOH and Their Antinemic Activity against Meloidogyne incognita. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Iliff AJ, Wang C, Ronan EA, Hake AE, Guo Y, Li X, Zhang X, Zheng M, Liu J, Grosh K, Duncan RK, Xu XZS. The nematode C. elegans senses airborne sound. Neuron 2021; 109:3633-3646.e7. [PMID: 34555314 PMCID: PMC8602785 DOI: 10.1016/j.neuron.2021.08.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 11/26/2022]
Abstract
Unlike olfaction, taste, touch, vision, and proprioception, which are
widespread across animal phyla, hearing is found only in vertebrates and some
arthropods. The vast majority of invertebrate species are thus considered
insensitive to sound. Here, we challenge this conventional view by showing that
the earless nematode C. elegans senses airborne sound at
frequencies reaching the kHz range. Sound vibrates C. elegans
skin, which acts as a pressure-to-displacement transducer similar to vertebrate
eardrum, activates sound-sensitive FLP/PVD neurons attached to the skin, and
evokes phonotaxis behavior. We identified two nAChRs that transduce sound
signals independently of ACh, revealing an unexpected function of nAChRs in
mechanosensation. Thus, the ability to sense airborne sound is not restricted to
vertebrates and arthropods as previously thought, and might have evolved
multiple times independently in the animal kingdom, suggesting convergent
evolution. Our studies also demonstrate that animals without ears may not be
presumed to be sound insensitive. Hearing is thought to exist only in vertebrates and some arthropods, but
not other animal phyla. Here, Xu and colleagues report that the earless nematode
C. elegans senses airborne sound and engages in phonotaxis.
Thus, hearing might have evolved multiple times independently in the animal
kingdom, suggesting convergent evolution.
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Affiliation(s)
- Adam J Iliff
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Can Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Elizabeth A Ronan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alison E Hake
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuling Guo
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xia Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xinxing Zhang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maohua Zheng
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianfeng Liu
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Karl Grosh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - R Keith Duncan
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - X Z Shawn Xu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA.
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17
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Wernet N, Wernet V, Fischer R. The small-secreted cysteine-rich protein CyrA is a virulence factor participating in the attack of Caenorhabditis elegans by Duddingtonia flagrans. PLoS Pathog 2021; 17:e1010028. [PMID: 34735554 PMCID: PMC8568293 DOI: 10.1371/journal.ppat.1010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/11/2021] [Indexed: 01/14/2023] Open
Abstract
Nematode-trapping fungi (NTF) are a diverse and intriguing group of fungi that live saprotrophically but can switch to a predatory lifestyle when starving and in the presence of nematodes. NTF like Arthrobotrys oligospora or Duddingtonia flagrans produce adhesive trapping networks to catch and immobilize nematodes. After penetration of the cuticle, hyphae grow and develop inside the worm and secrete large amounts of hydrolytic enzymes for digestion. In many microbial pathogenic interactions small-secreted proteins (SSPs) are used to manipulate the host. The genome of D. flagrans encodes more than 100 of such putative SSPs one of which is the cysteine-rich protein CyrA. We have chosen this gene for further analysis because it is only found in NTF and appeared to be upregulated during the interaction. We show that the cyrA gene was transcriptionally induced in trap cells, and the protein accumulated at the inner rim of the hyphal ring before Caenorhabditis elegans capture. After worm penetration, the protein appeared at the fungal infection bulb, where it is likely to be secreted with the help of the exocyst complex. A cyrA-deletion strain was less virulent, and the time from worm capture to paralysis was extended. Heterologous expression of CyrA in C. elegans reduced its lifespan. CyrA accumulated in C. elegans in coelomocytes where the protein possibly is inactivated. This is the first example that SSPs may be important in predatory microbial interactions.
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Affiliation(s)
- Nicole Wernet
- Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Karlsruhe, Germany
| | - Valentin Wernet
- Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Karlsruhe, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Dept. of Microbiology, Karlsruhe, Germany
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18
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Tóthné Bogdányi F, Boziné Pullai K, Doshi P, Erdős E, Gilián LD, Lajos K, Leonetti P, Nagy PI, Pantaleo V, Petrikovszki R, Sera B, Seres A, Simon B, Tóth F. Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review. Microorganisms 2021; 9:2130. [PMID: 34683451 PMCID: PMC8538326 DOI: 10.3390/microorganisms9102130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/28/2022] Open
Abstract
The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.
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Affiliation(s)
| | - Krisztina Boziné Pullai
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (K.B.P.); (R.P.)
| | - Pratik Doshi
- ImMuniPot Independent Research Group, H-2100 Gödöllő, Hungary
| | - Eszter Erdős
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (E.E.); (K.L.)
| | - Lilla Diána Gilián
- Szent István Campus Dormitories, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary;
| | - Károly Lajos
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (E.E.); (K.L.)
| | - Paola Leonetti
- Bari Unit, Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection of the CNR, 70126 Bari, Italy; (P.L.); (V.P.)
| | - Péter István Nagy
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Vitantonio Pantaleo
- Bari Unit, Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection of the CNR, 70126 Bari, Italy; (P.L.); (V.P.)
| | - Renáta Petrikovszki
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (K.B.P.); (R.P.)
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Bozena Sera
- Department of Environmental Ecology and Landscape Management, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia;
| | - Anikó Seres
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
| | - Barbara Simon
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary;
| | - Ferenc Tóth
- Department of Zoology and Ecology, Institute for Wildlife Management and Nature Conservation, Hungarian University of Agriculture and Life Sciences, H-2103 Gödöllő, Hungary; (P.I.N.); (A.S.)
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19
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Seong J, Shin J, Kim K, Cho BK. Microbial production of nematicidal agents for controlling plant-parasitic nematodes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Bubrig LT, Fierst JL. REVIEW OF THE DAUER HYPOTHESIS: WHAT NON-PARASITIC SPECIES CAN TELL US ABOUT THE EVOLUTION OF PARASITISM. J Parasitol 2021; 107:717-725. [PMID: 34525204 DOI: 10.1645/21-40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Parasitic lineages have acquired suites of new traits compared to their nearest free-living relatives. When and why did these traits arise? We can envision lineages evolving through multiple stable intermediate steps such as a series of increasingly exploitative species interactions. This view allows us to use non-parasitic species that approximate those intermediate steps to uncover the timing and original function of parasitic traits, knowledge critical to understanding the evolution of parasitism. The dauer hypothesis proposes that free-living nematode lineages evolved into parasites through two intermediate steps, phoresy and necromeny. Here we delve into the proposed steps of the dauer hypothesis by collecting and organizing data from genetic, behavioral, and ecological studies in a range of nematode species. We argue that hypotheses on the evolution of parasites will be strengthened by complementing comparative genomic studies with ecological studies on non-parasites that approximate intermediate steps.
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Affiliation(s)
- Louis T Bubrig
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, Virginia 22904
| | - Janna L Fierst
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, Alabama 35487-0344
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21
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Nisa RU, Tantray AY, Kouser N, Allie KA, Wani SM, Alamri SA, Alyemeni MN, Wijaya L, Shah AA. Influence of ecological and edaphic factors on biodiversity of soil nematodes. Saudi J Biol Sci 2021; 28:3049-3059. [PMID: 34025181 PMCID: PMC8117023 DOI: 10.1016/j.sjbs.2021.02.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Abstract
Nematodes are the most diverse and highly significant group of soil-inhabiting microorganisms that play a vital role in organic material decomposition and nutrient recycling. Diverse geographical locations and environmental gradients show a significant impact on the diversity of nematodes. Present study aims to assess the effects of ecological (altitude, temperature, moisture) and edaphic (soil pH, nutrients, soil patches) factors on the soil nematode diversity and structure at five different landscape patches (forests, apple orchards, rice fields, pastures, and alpine zone) from ten different sites of Kashmir valley (India). Differences in the altitudinal gradients results in the shift of generic nematode population. Among the soil patches, highest nematode diversity was observed in forest soil and least in alpine soil; however, bacteriovorous nematodes dominated all the soil patches. The temperature and moisture have a significant effect on nematode diversity, the highest nematode trophic levels were observed above 21°C temperature, and 30% moisture. Nematode abundance decreased from alkaline to acidic pH of the soil. Soil nutrients such as, nitrogen (N) and phosphorus (P) have shown a detrimental effect in nematode richness at each site, where nematode diversity and richness of genera were higher at abundant soil N and P but decreased at low soil nutrients. Ecological indices like diversity index (DI), Shannon-Wiener Index (H'), enrichment index (EI), and maturity Index (MI) values demonstrated forest soil more favourable for nematodes and high soil health status than other soil patches. This study suggested that these indices may be helpful as soil monitoring tools and assessing ecosystem sustainability and biodiversity.
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Affiliation(s)
- Rawhat Un Nisa
- Nematode Biodiversity & Genomics Research Lab. BGSB University, Rajouri 185234, India
| | - Aadil Yousuf Tantray
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB243UU, UK
| | - Nazia Kouser
- Nematode Biodiversity & Genomics Research Lab. BGSB University, Rajouri 185234, India
| | - Kaisar Ahmad Allie
- Nematode Biodiversity & Genomics Research Lab. BGSB University, Rajouri 185234, India
| | - Shaheen Majeed Wani
- Nematode Biodiversity & Genomics Research Lab. BGSB University, Rajouri 185234, India
| | - Saud A Alamri
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Nasser Alyemeni
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Leonard Wijaya
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Biology, Institut Teknologi Sumatera, Jalan Terusan Ryacudu, Way Hui, Jati Agung, South Lampung 35365, Indonesia
| | - Ali Asghar Shah
- Nematode Biodiversity & Genomics Research Lab. BGSB University, Rajouri 185234, India
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22
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Hartman JH, Widmayer SJ, Bergemann CM, King DE, Morton KS, Romersi RF, Jameson LE, Leung MCK, Andersen EC, Taubert S, Meyer JN. Xenobiotic metabolism and transport in Caenorhabditis elegans. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2021; 24:51-94. [PMID: 33616007 PMCID: PMC7958427 DOI: 10.1080/10937404.2021.1884921] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Caenorhabditis elegans has emerged as a major model in biomedical and environmental toxicology. Numerous papers on toxicology and pharmacology in C. elegans have been published, and this species has now been adopted by investigators in academic toxicology, pharmacology, and drug discovery labs. C. elegans has also attracted the interest of governmental regulatory agencies charged with evaluating the safety of chemicals. However, a major, fundamental aspect of toxicological science remains underdeveloped in C. elegans: xenobiotic metabolism and transport processes that are critical to understanding toxicokinetics and toxicodynamics, and extrapolation to other species. The aim of this review was to initially briefly describe the history and trajectory of the use of C. elegans in toxicological and pharmacological studies. Subsequently, physical barriers to chemical uptake and the role of the worm microbiome in xenobiotic transformation were described. Then a review of what is and is not known regarding the classic Phase I, Phase II, and Phase III processes was performed. In addition, the following were discussed (1) regulation of xenobiotic metabolism; (2) review of published toxicokinetics for specific chemicals; and (3) genetic diversity of these processes in C. elegans. Finally, worm xenobiotic transport and metabolism was placed in an evolutionary context; key areas for future research highlighted; and implications for extrapolating C. elegans toxicity results to other species discussed.
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Affiliation(s)
- Jessica H Hartman
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Samuel J Widmayer
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States
| | | | - Dillon E King
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Katherine S Morton
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Riccardo F Romersi
- Nicholas School of the Environment, Duke University, Durham, North Carolina
| | - Laura E Jameson
- School of Mathematical and Natural Sciences, Arizona State University - West Campus, Glendale, Arizona, United States
| | - Maxwell C K Leung
- School of Mathematical and Natural Sciences, Arizona State University - West Campus, Glendale, Arizona, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States
| | - Stefan Taubert
- Dept. Of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, the University of British Colombia, Vancouver, BC, Canada
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, North Carolina
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23
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Nematode epibionts on skin of the Florida manatee, Trichechus manatus latirostris. Sci Rep 2021; 11:1211. [PMID: 33441692 PMCID: PMC7806751 DOI: 10.1038/s41598-020-79879-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022] Open
Abstract
A survey for the presence of nematodes on the skin of the native Florida manatee, Trichechus manatus latirostris from Crystal River, Florida was conducted during annual manatee health assessments. A putative isolate of Cutidiplogaster manati (Diplogastridae) and two other nematodes belonging to the same family were recovered from mid-dorsal tail skin-scrapings from all sampled winter-collected healthy wild adult manatees during two successive years (2018–2019). Qualitative abundance estimates of these three species of diplogastrid nematodes suggest that an average wild Florida manatee adult might possess between 30,000 and 120,000 nematodes on its tail dorsum and that the entire body dorsum including the tail might possess 160,000–640,000 nematodes in roughly equal ratios. Attempts to culture these nematodes on a variety of different culture media were unsuccessful but examination of the mouth (stomatal) morphology suggests specialized feeding on microbes such as diatoms or predation on other nematodes. No skin lesions were observed during the 2018–2019 samplings suggesting that under normal conditions these nematodes are highly specialized free-living epibionts of the skin that are tightly bound to this niche and horizontally transferred between individual manatees in an analogous fashion to human skin mites (Demodex folliculorum and D. brevis). Molecular phylogenetic inferences using sequences of near full length SSU and D2–D3 expansion segments of LSU rRNA genes revealed a putative new morphospecies in Cutidiplogaster sister to C. manati that was monophyletic with several named Mononchoides species, and another putative new morphospecies that formed a clade with several undescribed species similar in appearance to Mononchoides as well as Tylopharyx, Eudiplogasterium, Paroigolaimella and Sachsia.
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Vanhamme L, Souopgui J, Ghogomu S, Ngale Njume F. The Functional Parasitic Worm Secretome: Mapping the Place of Onchocerca volvulus Excretory Secretory Products. Pathogens 2020; 9:pathogens9110975. [PMID: 33238479 PMCID: PMC7709020 DOI: 10.3390/pathogens9110975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 01/15/2023] Open
Abstract
Nematodes constitute a very successful phylum, especially in terms of parasitism. Inside their mammalian hosts, parasitic nematodes mainly dwell in the digestive tract (geohelminths) or in the vascular system (filariae). One of their main characteristics is their long sojourn inside the body where they are accessible to the immune system. Several strategies are used by parasites in order to counteract the immune attacks. One of them is the expression of molecules interfering with the function of the immune system. Excretory-secretory products (ESPs) pertain to this category. This is, however, not their only biological function, as they seem also involved in other mechanisms such as pathogenicity or parasitic cycle (molting, for example). We will mainly focus on filariae ESPs with an emphasis on data available regarding Onchocerca volvulus, but we will also refer to a few relevant/illustrative examples related to other worm categories when necessary (geohelminth nematodes, trematodes or cestodes). We first present Onchocerca volvulus, mainly focusing on the aspects of this organism that seem relevant when it comes to ESPs: life cycle, manifestations of the sickness, immunosuppression, diagnosis and treatment. We then elaborate on the function and use of ESPs in these aspects.
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Affiliation(s)
- Luc Vanhamme
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
- Correspondence:
| | - Jacob Souopgui
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
| | - Stephen Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, University of Buea, Buea P.O Box 63, Cameroon;
| | - Ferdinand Ngale Njume
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de Bruxelles, Rue des Professeurs Jeener et Brachet 12, 6041 Gosselies, Belgium; (J.S.); (F.N.N.)
- Molecular and Cell Biology Laboratory, Biotechnology Unit, University of Buea, Buea P.O Box 63, Cameroon;
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Abstract
Background: The more than 4100 species of phytoparasitic nematodes are responsible for an estimated economic loss in the agricultural sector of nearly $125 billion annually. Knowing the main lines of research and concerns about nematodes that affect plants is fundamental. Methods: For this reason, an analysis using bibliometric data has been carried out, with the aim of tracing the state of world research in this field, as well as knowing the main lines of work, their priorities, and their evolution. Results: This will allow us to establish strategic lines for the future development of this research. Conclusions: The analysis has allowed us to detect that the interest in nematodes affecting plants has not stopped growing in the last decades, and that tomato, soybean, and potato crops are the ones that generate the most interest, as well as nematodes of the genus Meloidogyne and Globodera. Likewise, we have detected that the main lines of research in this field are focused on biological control and host–parasite interaction.
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Schratzberger M, Holterman M, van Oevelen D, Helder J. A Worm's World: Ecological Flexibility Pays Off for Free-Living Nematodes in Sediments and Soils. Bioscience 2019; 69:867-876. [PMID: 31719709 PMCID: PMC6829015 DOI: 10.1093/biosci/biz086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Free-living nematodes, an ancient animal phylum of unsegmented microscopic roundworms, have successfully adapted to nearly every ecosystem on Earth: from marine and freshwater to land, from the polar regions to the tropics, and from the mountains to the ocean depths. They are globally the most abundant animals in sediments and soils. In the present article, we identify the factors that collectively explain the successful ecological proliferation of free-living nematodes and demonstrate the impact they have on vital sediment and soil processes. The ecological success of nematodes is strongly linked to their ability to feed on various food sources that are present in both sediments and soils, and to proliferate rapidly and survive in contrasting environmental conditions. The adaptations, roles, and behaviors of free-living nematodes have important implications for the resilience of sediments and soils, and for emergent animal communities responding to human alterations to ecosystems worldwide.
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Affiliation(s)
| | - Martijn Holterman
- Laboratory of Nematology, Wageningen University, Wageningen, the Netherlands
| | | | - Johannes Helder
- Laboratory of Nematology, Wageningen University, Wageningen, the Netherlands
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Helms SJ, Rozemuller WM, Costa AC, Avery L, Stephens GJ, Shimizu TS. Modelling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behaviour across species. J R Soc Interface 2019; 16:20190174. [PMID: 31455164 DOI: 10.1098/rsif.2019.0174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A quantitative understanding of organism-level behaviour requires predictive models that can capture the richness of behavioural phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here, we investigate the motile behaviour of nematodes at the level of their translational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioural repertoire by measuring motile trajectories of the canonical laboratory strain Caenorhabditis elegans N2 as well as wild strains and distant species. We focus on trajectory dynamics over time scales spanning the transition from ballistic (straight) to diffusive (random) movement and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bearing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioural control and a trade-off between exploration and exploitation. The distribution of phenotypes along this primary mode of variation reveals that not only the mean but also the variance varies considerably across strains, suggesting that these nematode lineages employ contrasting 'bet-hedging' strategies for foraging.
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Affiliation(s)
| | | | - Antonio Carlos Costa
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
| | - Leon Avery
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
| | - Greg J Stephens
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands.,Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan
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Presence or absence? Primary structure, regioselectivity and evolution of Δ12/ω3 fatty acid desaturases in nematodes. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1194-1205. [PMID: 31108204 DOI: 10.1016/j.bbalip.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/12/2019] [Accepted: 05/10/2019] [Indexed: 11/21/2022]
Abstract
For vertebrates, the adequate supply of polyunsaturated fatty acids (PUFA) by the diet, in particular ω3 long-chain PUFA, is considered essential for neural development, growth and reproduction. In contrast to aquatic ecosystems, ω3 long-chain PUFA apparently are not widely available in the terrestrial food chain. Their de novo synthesis requires the presence of Δ12 and ω3 fatty acid desaturase enzymes, which are absent in vertebrates but present, for example, in the nematode Caenorhabditis elegans (FAT-2 and FAT-1). This raises the question if soil-dwelling nematodes offer substantial supply of these valuable nutritional compounds in terrestrial food webs. BLAST searches in available nematode genomes revealed the existence of fat-2 like genes in almost all clade III-V species, but failed to identify orthologs in clade I-II nematodes. An additional RT-PCR screen across soil-dwelling nematode species identified six novel fat-2 like genes. Hints for the genetic basis of a ω3 (fat-1) desaturase activity was found only in selected clade IV-V species, but not in clades I to III nematodes. Fatty acid pattern analyses following a PUFA-free cultivation and enzymatic characterization of six selected fat-2 or fat-1 like desaturases in yeast confirmed the findings from the genetic approaches. Thus, in similar soil habitats, taxa exist that can synthesize ω3 long-chain PUFA (as Panagrolaimus, Mesorhabditis and Caenorhabditis) whereas others are unable to do so (Acrobeloides, Cephalobus and Oscheius). While these nematodes do not differ in trophic position or major diet, distinction in reproduction mode may have led to the observed variations in desaturase genes.
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Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes. PLoS One 2019; 14:e0214554. [PMID: 30917179 PMCID: PMC6436744 DOI: 10.1371/journal.pone.0214554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Novel chemical controls are needed that selectively target human, animal, and plant parasitic nematodes with reduced adverse effects on the host or the environment. We hypothesize that the phosphodiesterase (PDE) enzyme family represents a potential target for development of novel nematicides and anthelmintics. To test this, we identified six PDE families present in the nematode phylum that are orthologous to six of the eleven human PDE families. We characterized the binding interactions of family-selective PDE inhibitors with human and C. elegans PDE4 in conjunction with molecular dynamics (MD) simulations to evaluate differences in binding interactions of these inhibitors within the PDE4 catalytic domain. We observed that roflumilast (human PDE4-selective inhibitor) and zardaverine (selective for human PDE3 and PDE4) were 159- and 77-fold less potent, respectively, in inhibiting C. elegans PDE4. The pan-specific PDE inhibitor isobutyl methyl xanthine (IBMX) had similar affinity for nematode and human PDE4. Of 32 residues within 5 Å of the ligand binding site, five revealed significant differences in non-bonded interaction energies (van der Waals and electrostatic interaction energies) that could account for the differential binding affinities of roflumilast and zardaverine. One site (Phe506 in the human PDE4D3 amino acid sequence corresponding to Tyr253 in C. elegans PDE4) is predicted to alter the binding conformation of roflumilast and zardaverine (but not IBMX) into a less energetically favorable state for the nematode enzyme. The pharmacological differences in sensitivity to PDE4 inhibitors in conjunction with differences in the amino acids comprising the inhibitor binding sites of human and C. elegans PDE4 catalytic domains together support the feasibility of designing the next generation of anthelmintics/nematicides that could selectively bind to nematode PDEs.
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Youssar L, Wernet V, Hensel N, Yu X, Hildebrand HG, Schreckenberger B, Kriegler M, Hetzer B, Frankino P, Dillin A, Fischer R. Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans. PLoS Genet 2019; 15:e1008029. [PMID: 30917129 PMCID: PMC6453484 DOI: 10.1371/journal.pgen.1008029] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/08/2019] [Accepted: 02/18/2019] [Indexed: 11/21/2022] Open
Abstract
Nematode-trapping fungi (NTF) are a large and diverse group of fungi, which may switch from a saprotrophic to a predatory lifestyle if nematodes are present. Different fungi have developed different trapping devices, ranging from adhesive cells to constricting rings. After trapping, fungal hyphae penetrate the worm, secrete lytic enzymes and form a hyphal network inside the body. We sequenced the genome of Duddingtonia flagrans, a biotechnologically important NTF used to control nematode populations in fields. The 36.64 Mb genome encodes 9,927 putative proteins, among which are more than 638 predicted secreted proteins. Most secreted proteins are lytic enzymes, but more than 200 were classified as small secreted proteins (< 300 amino acids). 117 putative effector proteins were predicted, suggesting interkingdom communication during the colonization. As a first step to analyze the function of such proteins or other phenomena at the molecular level, we developed a transformation system, established the fluorescent proteins GFP and mCherry, adapted an assay to monitor protein secretion, and established gene-deletion protocols using homologous recombination or CRISPR/Cas9. One putative virulence effector protein, PefB, was transcriptionally induced during the interaction. We show that the mature protein is able to be imported into nuclei in Caenorhabditis elegans cells. In addition, we studied trap formation and show that cell-to-cell communication is required for ring closure. The availability of the genome sequence and the establishment of many molecular tools will open new avenues to studying this biotechnologically relevant nematode-trapping fungus. Nematode-trapping fungi are fascinating microorganisms, because they are able to switch from saprotrophic growth to a predatory lifestyle. Duddingtonia flagrans forms adhesive trap systems and conidia and resistant chlamydospores. Chlamydospores are ideal for dissemination in the environment to control nematode populations in the field. We show that D. flagrans is able to catch C. elegans but also the very large wine-pathogenic nematode Xiphinema index. We sequenced the D. flagrans genome and show that it encodes about 10,000 genes with a large proportion of secreted proteins. We hypothesize that virulence effector proteins are involved in the interkingdom organismic interaction and identified more than 100 candidates. In order to investigate the molecular biology of D. flagrans and its interaction with nematodes, we established a transformation system and several molecular tools. We show that cell-to-cell communication and hyphal fusion are required for trap formation. Finally, we show that one putative virulence effector protein targets nuclei when expressed in C. elegans.
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Affiliation(s)
- Loubna Youssar
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Valentin Wernet
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Nicole Hensel
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Xi Yu
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Heinz-Georg Hildebrand
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Birgit Schreckenberger
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Marius Kriegler
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | | | - Phillip Frankino
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of Berkeley, Berkeley, California, United States of America
| | - Andrew Dillin
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of Berkeley, Berkeley, California, United States of America
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology (KIT)—South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
- * E-mail:
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Haag ES, Fitch DHA, Delattre M. From "the Worm" to "the Worms" and Back Again: The Evolutionary Developmental Biology of Nematodes. Genetics 2018; 210:397-433. [PMID: 30287515 PMCID: PMC6216592 DOI: 10.1534/genetics.118.300243] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | | | - Marie Delattre
- Laboratoire de Biologie Moléculaire de la Cellule, CNRS, INSERM, Ecole Normale Supérieure de Lyon, 69007, France
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Abstract
The nematode Caenorhabditis elegans is a simple metazoan animal that is widely used as a model to understand the genetic control of development. The completely sequenced C. elegans genome contains 22 T-box genes, and they encode factors that show remarkable diversity in sequence, DNA-binding specificity, and function. Only three of the C. elegans T-box factors can be grouped into the conserved subfamilies found in other organisms, while the remaining factors are significantly diverged and unlike those in most other animals. While some of the C. elegans factors can bind canonical T-box binding elements, others bind and regulate target gene expression through distinct sequences. The nine genetically characterized T-box factors have varied functions in development and morphogenesis of muscle, hypodermal tissues, and neurons, as well as in early blastomere fate specification, cell migration, apoptosis, and sex determination, but the functions of most of the C. elegans T-box factors have not yet been extensively characterized. Like T-box factors in other animals, interaction with a Groucho-family corepressor and posttranslational SUMOylation have been shown to affect C. elegans T-box factor activity, and it is likely that additional mechanisms affecting T-box factor activity will be discovered using the effective genetic approaches in this organism.
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Jay Burr AH, Baldwin JG. The nematode stoma: Homology of cell architecture with improved understanding by confocal microscopy of labeled cell boundaries. J Morphol 2016; 277:1168-86. [DOI: 10.1002/jmor.20567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/24/2016] [Accepted: 05/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- A. H. Jay Burr
- Department of Biological Sciences; Simon Fraser University; Burnaby British Columbia V5A 1S6 Canada
- Department of Nematology; University of California; Riverside California 92521
| | - James G. Baldwin
- Department of Nematology; University of California; Riverside California 92521
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The evolution of tyrosine-recombinase elements in Nematoda. PLoS One 2014; 9:e106630. [PMID: 25197791 PMCID: PMC4157794 DOI: 10.1371/journal.pone.0106630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/04/2014] [Indexed: 12/28/2022] Open
Abstract
Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.
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