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Skalon EK, Starunov VV, Slyusarev GS. RNA-seq analysis of parasitism by Intoshia linei (Orthonectida) reveals protein effectors of defence, communication, feeding and growth. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:398-405. [PMID: 38369898 DOI: 10.1002/jez.b.23247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
Orthonectida is a group of multicellular endoparasites of a wide range of marine invertebrates. Their parasitic stage is a multinuclear shapeless plasmodium infiltrating host tissues. The development of the following worm-like sexual generation takes place within the cytoplasm of the plasmodium. The existence of the plasmodial stage and the development of a sexual stage within the plasmodium are unique features to Bilateria. However, the molecular mechanisms that maintain this peculiar organism, and hence enable parasitism in orthonectids, are unknown. Here, we present the first-ever RNA-seq analysis of the plasmodium, aimed at the identification and characterization of the plasmodium-specific protein-coding genes and corresponding hypothetical proteins that distinguish the parasitic plasmodium stage from the sexual stage of the orthonectid Intoshia linei Giard, 1877, parasite of nemertean Lineus ruber Müller, 1774. We discovered 119 plasmodium-specific proteins, 82 of which have inferred functions based on known domains. Thirty-five of the detected proteins are orphans, at least part of which may reflect the unique evolutionary adaptations of orthonectids to parasitism. Some of the identified proteins are known effector molecules of other endoparasites suggesting convergence. Our data indicate that the plasmodium-specific proteins might be involved in the plasmodium defense against the host, host-parasite communication, feeding and nutrient uptake, growth within the host, and support of the sexual stage development. These molecular processes in orthonectids have not been described before, and the particular protein effectors remained unknown until now.
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Affiliation(s)
- Elizaveta K Skalon
- Department of Invertebrate Zoology, Faculty of Biology, St Petersburg University, St. Petersburg, Russia
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, St Petersburg University, St. Petersburg, Russia
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - George S Slyusarev
- Department of Invertebrate Zoology, Faculty of Biology, St Petersburg University, St. Petersburg, Russia
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Price DRG, Steele P, Frew D, McLean K, Androscuk D, Geldhof P, Borloo J, Albaladejo JP, Nisbet AJ, McNeilly TN. Characterisation of protective vaccine antigens from the thiol-containing components of excretory/secretory material of Ostertagia ostertagi. Vet Parasitol 2024; 328:110154. [PMID: 38490160 DOI: 10.1016/j.vetpar.2024.110154] [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: 11/21/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024]
Abstract
Previous vaccination trials have demonstrated that thiol proteins affinity purified from Ostertagia ostertagi excretory-secretory products (O. ostertagi ES-thiol) are protective against homologous challenge. Here we have shown that protection induced by this vaccine was consistent across four independent vaccine-challenge experiments. Protection is associated with reduced cumulative faecal egg counts across the duration of the trials, relative to control animals. To better understand the diversity of antigens in O. ostertagi ES-thiol we used high-resolution shotgun proteomics to identify 490 unique proteins in the vaccine preparation. The most numerous ES-thiol proteins, with 91 proteins identified, belong to the sperm-coating protein/Tpx/antigen 5/pathogenesis-related protein 1 (SCP/TAPS) family. This family includes previously identified O. ostertagi vaccine antigens O. ostertagi ASP-1 and ASP-2. The ES-thiol fraction also has numerous proteinases, representing three distinct classes, including: metallo-; aspartyl- and cysteine proteinases. In terms of number of family members, the M12 astacin-like metalloproteinases, with 33 proteins, are the most abundant proteinase family in O. ostertagi ES-thiol. The O. ostertagi ES-thiol proteome provides a comprehensive database of proteins present in this vaccine preparation and will guide future vaccine antigen discovery projects.
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Affiliation(s)
- Daniel R G Price
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK.
| | - Philip Steele
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - David Frew
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Kevin McLean
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Dorota Androscuk
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Peter Geldhof
- Laboratory of Parasitology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Sciences, Ghent University, Belgium
| | - Jimmy Borloo
- Laboratory of Parasitology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Sciences, Ghent University, Belgium
| | - Javier Palarea Albaladejo
- Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, Scotland, UK; Department of Computer Science, Applied Mathematics and Statistics, University of Girona, Girona, Spain
| | - Alasdair J Nisbet
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
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Zhuang XM, Guo ZY, Zhang M, Chen YH, Qi FN, Wang RQ, Zhang L, Zhao PJ, Lu CJ, Zou CG, Ma YC, Xu J, Zhang KQ, Cao YR, Liang LM. Ethanol mediates the interaction between Caenorhabditis elegans and the nematophagous fungus Purpureocillium lavendulum. Microbiol Spectr 2023; 11:e0127023. [PMID: 37560934 PMCID: PMC10580998 DOI: 10.1128/spectrum.01270-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
Accurately recognizing pathogens by the host is vital for initiating appropriate immune response against infecting microorganisms. Caenorhabditis elegans has no known receptor to recognize pathogen-associated molecular pattern. However, recent studies showed that nematodes have a strong specificity for transcriptomes infected by different pathogens, indicating that they can identify different pathogenic microorganisms. However, the mechanism(s) for such specificity remains largely unknown. In this study, we showed that the nematophagous fungus Purpureocillium lavendulum can infect the intestinal tract of the nematode C. elegans and the infection led to the accumulation of reactive oxygen species (ROS) in the infected intestinal tract, which suppressed fungal growth. Co-transcriptional analysis revealed that fungal genes related to anaerobic respiration and ethanol production were up-regulated during infection. Meanwhile, the ethanol dehydrogenase Sodh-1 in C. elegans was also up-regulated. Together, these results suggested that the infecting fungi encounter hypoxia stress in the nematode gut and that ethanol may play a role in the host-pathogen interaction. Ethanol production in vitro during fungal cultivation in hypoxia conditions was confirmed by gas chromatography-mass spectrometry. Direct treatment of C. elegans with ethanol elevated the sodh-1 expression and ROS accumulation while repressing a series of immunity genes that were also repressed during fungal infection. Mutation of sodh-1 in C. elegans blocked ROS accumulation and increased the nematode's susceptibility to fungal infection. Our study revealed a new recognition and antifungal mechanism in C. elegans. The novel mechanism of ethanol-mediated interaction between the fungus and nematode provides new insights into fungal pathogenesis and for developing alternative biocontrol of pathogenic nematodes by nematophagous fungi. IMPORTANCE Nematodes are among the most abundant animals on our planet. Many of them are parasites in animals and plants and cause human and animal health problems as well as agricultural losses. Studying the interaction of nematodes and their microbial pathogens is of great importance for the biocontrol of animal and plant parasitic nematodes. In this study, we found that the model nematode Caenorhabditis elegans can recognize its fungal pathogen, the nematophagous fungus Purpureocillium lavendulum, through fungal-produced ethanol. Then the nematode elevated the reactive oxygen species production in the gut to inhibit fungal growth in an ethanol dehydrogenase-dependent manner. With this mechanism, novel biocontrol strategies may be developed targeting the ethanol receptor or metabolic pathway of nematodes. Meanwhile, as a volatile organic compound, ethanol should be taken seriously as a vector molecule in the microbial-host interaction in nature.
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Affiliation(s)
- Xue-Mei Zhuang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Zhi-Yi Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Meng Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Yong-Hong Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Feng-Na Qi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Ren-Qiao Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Ling Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Pei-Ji Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Chao-Jun Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Cheng-Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Yi-Cheng Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Yan-Ru Cao
- College of Agriculture and Life Sciences, Kunming University, Kunming, China
| | - Lian-Ming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
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Hassan SU, Chua EG, Paz EA, Tay CY, Greeff JC, Palmer DG, Dudchenko O, Aiden EL, Martin GB, Kaur P. Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock. BMC Genomics 2023; 24:74. [PMID: 36792983 PMCID: PMC9933375 DOI: 10.1186/s12864-023-09172-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics. RESULTS We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus. CONCLUSION This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development.
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Affiliation(s)
- Shamshad Ul Hassan
- grid.1012.20000 0004 1936 7910UWA School of Agriculture and Environment, The University of Western Australia, 6009 Crawley, WA Australia ,grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Eng Guan Chua
- grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Erwin A. Paz
- grid.1012.20000 0004 1936 7910UWA School of Agriculture and Environment, The University of Western Australia, 6009 Crawley, WA Australia ,grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Chin Yen Tay
- grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Johan C. Greeff
- grid.493004.aDepartment of Primary Industries and Regional Development, Western Australia 3 Baron Hay Court, South Perth, 6151 WA Australia
| | - Dieter G. Palmer
- grid.493004.aDepartment of Primary Industries and Regional Development, Western Australia 3 Baron Hay Court, South Perth, 6151 WA Australia
| | - Olga Dudchenko
- grid.39382.330000 0001 2160 926XThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston, TX USA ,grid.21940.3e0000 0004 1936 8278Center for Theoretical Biological Physics, Rice University, 77005 Houston, TX USA
| | - Erez Lieberman Aiden
- grid.39382.330000 0001 2160 926XThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston, TX USA ,grid.21940.3e0000 0004 1936 8278Center for Theoretical Biological Physics, Rice University, 77005 Houston, TX USA ,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong China ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Graeme B. Martin
- grid.1012.20000 0004 1936 7910UWA School of Agriculture and Environment, The University of Western Australia, 6009 Crawley, WA Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia.
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5
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Gibson SB, Ness-Cohn E, Andersen EC. Benzimidazoles cause lethality by inhibiting the function of Caenorhabditis elegans neuronal beta-tubulin. Int J Parasitol Drugs Drug Resist 2022; 20:89-96. [PMID: 36332489 PMCID: PMC9771835 DOI: 10.1016/j.ijpddr.2022.10.004] [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: 07/19/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/08/2022]
Abstract
Parasitic nematode infections cause an enormous global burden to both humans and livestock. Resistance to the limited arsenal of anthelmintic drugs used to combat these infections is widespread, including benzimidazole (BZ) compounds. Previous studies using the free-living nematode Caenorhabditis elegans to model parasitic nematode resistance have shown that loss-of-function mutations in the beta-tubulin gene ben-1 confer resistance to BZ drugs. However, the mechanism of resistance and the tissue-specific susceptibility are not well known in any nematode species. To identify in which tissue(s) ben-1 function underlies BZ susceptibility, transgenic strains that express ben-1 in different tissues, including hypodermis, muscles, neurons, intestine, and ubiquitous expression were generated. High-throughput fitness assays were performed to measure and compare the quantitative responses to BZ compounds among different transgenic lines. Significant BZ susceptibility was observed in animals expressing ben-1 in neurons, comparable to expression using the ben-1 promoter. This result suggests that ben-1 function in neurons underlies susceptibility to BZ. Subsetting neuronal expression of ben-1 based on the neurotransmitter system further restricted ben-1 function in cholinergic neurons to cause BZ susceptibility. These results better inform our current understanding of the cellular mode of action of BZs and also suggest additional treatments that might potentiate the effects of BZs in neurons.
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Affiliation(s)
- Sophia B. Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Elan Ness-Cohn
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA,Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, IL, 60611, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA,Corresponding author. Department of Molecular Biosciences Northwestern University 4619 Silverman Hall 2205 Tech Drive Evanston, IL, 60208, USA.
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Thuma N, Döhler D, Mielenz D, Sticht H, Radtke D, Reimann L, Warscheid B, Voehringer D. A newly identified secreted larval antigen elicits basophil-dependent protective immunity against N. brasiliensis infection. Front Immunol 2022; 13:979491. [PMID: 36091065 PMCID: PMC9453252 DOI: 10.3389/fimmu.2022.979491] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022] Open
Abstract
Hookworms infect more that 400 million people and cause significant socio-economic burden on endemic countries. The lack of efficient vaccines and the emergence of anthelminthic drug resistance are of major concern. Free-living hookworm larvae infect their hosts via the skin and live as adult worms in the small intestine where they feed on host tissue and blood. Excretory/secretory (E/S) products, released by helminths as they migrate through their host, are thought to play a key role in facilitating infection and successful establishment of parasitism. However, E/S products can also elicit protective immune responses that might be harnessed for vaccine development. By performing Western blots with serum of Nippostrongylus brasiliensis (Nb) infected mice as a model for human hookworm infection, we identified a largely overlapping set of IgG1- and IgE-reactive antigens in E/S from infective L3 stage larvae. Mass spectrometry analysis led to the identification of a new protein family with 6 paralogues in the Nb genome which we termed Nb-LSA1 for “Nippostrongylus brasiliensis larval secreted protein 1”. The recombinantly expressed 17 kDa family member Nb-LSA1a was recognized by antibodies in the serum of Nb immune mice. Immunization of mice with Nb-LSA1a in alum elicited a strong IgG1 response but no detectable antigen-specific IgE. Most importantly, immunized mice were largely protected against a challenge Nb infection. This effect was dependent on the presence of basophils and occurred before the parasites reached the intestine. Therefore, basophils appear to play a critical role for rapid control of infection with L3 stage larvae in mice immunized with a single secreted larval protein. A better understanding of basophil-mediated protective immunity and identification of potent larval antigens of human hookworms could help to develop promising vaccination strategies.
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Affiliation(s)
- Natalie Thuma
- Department of Infection Biology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Daniela Döhler
- Department of Infection Biology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Daniel Radtke
- Department of Infection Biology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Lena Reimann
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - David Voehringer
- Department of Infection Biology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- *Correspondence: David Voehringer,
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Whole-genome sequencing and analysis of Streptomyces strains producing multiple antinematode drugs. BMC Genomics 2022; 23:610. [PMID: 35996099 PMCID: PMC9396898 DOI: 10.1186/s12864-022-08847-4] [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: 04/22/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022] Open
Abstract
Background Nematodes are parasitic animals that cause over 100 billion US dollars loss in agricultural business. The whole-genomes of two Streptomyces strains, Streptomyces spectabilis KCTC9218T and Streptomyces sp. AN091965, were sequenced. Both strains produce spectinabilin, an antinematode drug. Its secondary metabolism was examined to aid the development of an efficient nematicidal drug-producing host strain. Results The whole-genome sequences of S. spectabilis KCTC9218T and Streptomyces sp. AN091965 were analyzed using PacBio and Illumina sequencing platforms, and assembled using hybrid methodology. The total contig lengths for KCTC9218T and AN091965 were 9.97 Mb and 9.84 Mb, respectively. A total of 8,374 and 8,054 protein-coding genes, as well as 39 and 45 secondary metabolite biosynthetic gene clusters were identified in KCTC9218T and AN091965, respectively. 18.4 ± 6.45 mg/L and 213.89 ± 21.30 mg/L of spectinabilin were produced by S. spectabilis KCTC9218T and Streptomyces sp. AN091965, respectively. Pine wilt disease caused by nematode was successfully prevented by lower concentration of spectinabilin injection than that of abamectin recommended by its manufacturer. Production of multiple antinematode drugs, including spectinabilin, streptorubin B, and undecylprodigiosin was observed in both strains using high-resolution liquid chromatography mass spectrometry (LC–MS) analysis. Conclusions Whole-genome sequencing of spectinabilin-producing strains, coupled with bioinformatics and mass spectrometry analyses, revealed the production of multiple nematicidal drugs in the KCTC9218T and AN091965 strains. Especially, Streptomyces sp. AN091965 showed high production level of spectinabilin, and this study provides crucial information for the development of potential nematicidal drug producers. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08847-4.
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Dube F, Hinas A, Roy S, Martin F, Åbrink M, Svärd S, Tydén E. Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro. Parasit Vectors 2022; 15:158. [PMID: 35513885 PMCID: PMC9074254 DOI: 10.1186/s13071-022-05260-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Background The nematode Parascaris univalens is one of the most prevalent parasitic pathogens infecting horses but anthelmintic resistance undermines treatment approaches. The molecular mechanisms underlying drug activity and resistance remain poorly understood in this parasite since experimental in vitro models are lacking. The aim of this study was to evaluate the use of Caenorhabditis elegans as a model for P. univalens drug metabolism/resistance studies by a comparative gene expression approach after in vitro exposure to the anthelmintic drug ivermectin (IVM). Methods Twelve adult P. univalens worms in groups of three were exposed to ivermectin (IVM, 10–13 M, 10–11 M, 10–9 M) or left unexposed for 24 h at 37 °C, and total RNA, extracted from the anterior end of the worms, was sequenced using Illumina NovaSeq. Differentially expressed genes (DEGs) involved in metabolism, transportation, or gene expression with annotated Caernorhabditis elegans orthologues were identified as candidate genes to be involved in IVM metabolism/resistance. Similarly, groups of 300 adult C. elegans worms were exposed to IVM (10–9 M, 10–8 M and 10–7 M) or left unexposed for 4 h at 20 °C. Quantitative RT-PCR of RNA extracted from the C. elegans worm pools was used to compare against the expression of selected P. univalens candidate genes after drug treatment. Results After IVM exposure, 1085 DEGs were found in adult P. univalens worms but the relative gene expression changes were small and large variabilities were found between different worms. Fifteen of the DEGs were chosen for further characterization in C. elegans after comparative bioinformatics analyses. Candidate genes, including the putative drug target lgc-37, responded to IVM in P. univalens, but marginal to no responses were observed in C. elegans despite dose-dependent behavioral effects observed in C. elegans after IVM exposure. Thus, the overlap in IVM-induced gene expression in this small set of genes was minor in adult worms of the two nematode species. Conclusion This is the first time to our knowledge that a comparative gene expression approach has evaluated C. elegans as a model to understand IVM metabolism/resistance in P. univalens. Genes in P. univalens adults that responded to IVM treatment were identified. However, identifying conserved genes in P. univalens and C. elegans involved in IVM metabolism/resistance by comparing gene expression of candidate genes proved challenging. The approach appears promising but was limited by the number of genes studied (n = 15). Future studies comparing a larger number of genes between the two species may result in identification of additional candidate genes involved in drug metabolism and/or resistance. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05260-4.
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Affiliation(s)
- Faruk Dube
- Division of Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7036, 750 07, Uppsala, Sweden.
| | - Andrea Hinas
- Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden
| | - Shweta Roy
- Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden
| | - Frida Martin
- Division of Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7036, 750 07, Uppsala, Sweden
| | - Magnus Åbrink
- Section of Immunology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7036, 750 07, Uppsala, Sweden
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden
| | - Eva Tydén
- Division of Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7036, 750 07, Uppsala, Sweden
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Secreted virulence factors from Heterorhabditis bacteriophora highlight its utility as a model parasite among Clade V nematodes. Int J Parasitol 2021; 51:321-325. [PMID: 33421438 DOI: 10.1016/j.ijpara.2020.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/23/2022]
Abstract
Much of the available knowledge of entomopathogenic virulence factors has been gleaned from studies in the nematode parasite Steinernema carpocapsae, but there is good reason to complement this knowledge with similar studies in Heterorhabditis bacteriophora. Three candidate virulence factors from H. bacteriophora have recently been characterised, and each was demonstrated to contribute to infection. This information can be used not only to advance efforts in the biocontrol of insect pests, but also to make inferences about the emergence of parasitism among Clade V nematodes.
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10
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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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11
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Villalobos-Segura MDC, García-Prieto L, Rico-Chávez O. Effects of latitude, host body size, and host trophic guild on patterns of diversity of helminths associated with humans, wild and domestic mammals of Mexico. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2020; 13:221-230. [PMID: 33224727 PMCID: PMC7666364 DOI: 10.1016/j.ijppaw.2020.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 11/29/2022]
Abstract
Parasites are strictly associated with their hosts and present a great diversity of life histories, often resulting in different diversity patterns than those observed in free-living species. However, ecological approaches have detected that, in some cases, mammal-associated helminths respond similarly to non-parasitic species in terms of diversity patterns. Using 2200 recorded interactions, we analysed the diversity patterns of helminths (Acanthocephala, Nematoda and Platyhelminthes) harbored by humans, wild and domestic mammals of Mexico, depending on latitude, host body mass and trophic guild (carnivore, herbivore, insectivore, omnivore), considering helminth richness and average taxonomic distinctness, and host phylogenetic diversity and phylogenetic clustering. Latitude was positively correlated with the average taxonomic distinctness encompassing the three parasite phyla and nematodes. Northern latitudes had less taxonomically related parasite assemblages. Host body mass had a significant negative relationship with the average taxonomic distinctness of acanthocephalans and the richness of helminths associated to wild hosts. The omnivore hosts had greater parasite richness, while insectivores had a less taxonomically related parasite assemblage and herbivores had a more heterogeneous parasite assemblage. Our results highlight the importance of incorporating different dimensions of diversity, such as average taxonomic distinctness and to consider the composition of parasite assemblages to better understand their diversity patterns. Four diversity measures were used to describe diversity patterns of helminths. Latitude was positively correlated with helminth average taxonomic distinctness. Host body mass was negatively related with the helminth richness of wildlife hosts. Helminth sets of omnivore hosts were richer in parasite species. Helminth sets of insectivore hosts had a wider taxonomic breadth.
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Affiliation(s)
- María Del Carmen Villalobos-Segura
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, 04510, México City, Mexico
| | - Luis García-Prieto
- Laboratorio de Helmintología, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-153, 04510, México City, Mexico
| | - Oscar Rico-Chávez
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, 04510, México City, Mexico
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12
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Hahnel SR, Dilks CM, Heisler I, Andersen EC, Kulke D. Caenorhabditis elegans in anthelmintic research - Old model, new perspectives. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:237-248. [PMID: 33249235 PMCID: PMC7704361 DOI: 10.1016/j.ijpddr.2020.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/13/2022]
Abstract
For more than four decades, the free-living nematode Caenorhabditis elegans has been extensively used in anthelmintic research. Classic genetic screens and heterologous expression in the C. elegans model enormously contributed to the identification and characterization of molecular targets of all major anthelmintic drug classes. Although these findings provided substantial insights into common anthelmintic mechanisms, a breakthrough in the treatment and control of parasitic nematodes is still not in sight. Instead, we are facing increasing evidence that the enormous diversity within the phylum Nematoda cannot be recapitulated by any single free-living or parasitic species and the development of novel broad-spectrum anthelmintics is not be a simple goal. In the present review, we summarize certain milestones and challenges of the C. elegans model with focus on drug target identification, anthelmintic drug discovery and identification of resistance mechanisms. Furthermore, we present new perspectives and strategies on how current progress in C. elegans research will support future anthelmintic research.
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Affiliation(s)
| | - Clayton M Dilks
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
| | | | - Erik C Andersen
- Northwestern University, Department of Molecular Biosciences, Evanston, IL, USA.
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13
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D’Amelio S, Lombardo F, Pizzarelli A, Bellini I, Cavallero S. Advances in Omic Studies Drive Discoveries in the Biology of Anisakid Nematodes. Genes (Basel) 2020; 11:E801. [PMID: 32679891 PMCID: PMC7397233 DOI: 10.3390/genes11070801] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/28/2023] Open
Abstract
Advancements in technologies employed in high-throughput next-generation sequencing (NGS) methods are supporting the spread of studies that, combined with advances in computational biology and bioinformatics, have greatly accelerated discoveries within basic and biomedical research for many parasitic diseases. Here, we review the most updated "omic" studies performed on anisakid nematodes, a family of marine parasites that are causative agents of the fish-borne zoonosis known as anisakiasis or anisakidosis. Few deposited data on Anisakis genomes are so far available, and this still hinders the deep and highly accurate characterization of biological aspects of interest, even as several transcriptomic and proteomic studies are becoming available. These have been aimed at discovering and characterizing molecules specific to peculiar developmental parasitic stages or tissues, as well as transcripts with pathogenic potential as toxins and allergens, with a broad relevance for a better understanding of host-pathogen relationships and for the development of reliable diagnostic tools.
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Affiliation(s)
| | | | | | | | - Serena Cavallero
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (S.D.); (F.L.); (A.P.); (I.B.)
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14
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Duguet TB, Soichot J, Kuzyakiv R, Malmström L, Tritten L. Extracellular Vesicle-Contained microRNA of C. elegans as a Tool to Decipher the Molecular Basis of Nematode Parasitism. Front Cell Infect Microbiol 2020; 10:217. [PMID: 32523895 PMCID: PMC7261840 DOI: 10.3389/fcimb.2020.00217] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023] Open
Abstract
Among the fundamental biological processes affected by microRNAs, small regulators of gene expression, a potential role in host-parasite communication is intriguing. We compared the miRNA complement of extracellular vesicles released by the free-living nematode Caenorhabditis elegans in culture to that of other adult parasitic nematodes. Expecting convergent functional roles for secreted miRNAs due to the common parasitic lifestyle of the organisms under investigation, we performed a miRNA sequence analysis as well as target search and pathway enrichment for potential mRNA targets within host immune functions. We found that the parasite miRNA seed sequences were more often identical to those of C. elegans, rather than to those of their hosts. However, we observed that the nematode-secreted miRNA fractions shared more often seed sequences with host miRNAs than those that are not found in the extracellular environment. Development and proliferation of immune cells was predicted to be affected several-fold by nematode miRNA release. In addition, we identified the AGE-RAGE signaling as a convergent targeted pathway by species-specific miRNAs from several parasitic species. We propose a multi-species comparative approach to differentiate those miRNAs that may have critical functions in host modulation, from those that may not. With our simple analysis, we put forward a workflow to study traits of parasitism at the miRNA level. This work will find even more resonance and significance, as an increasing amount of parasite miRNA collections are expected to be produced in the future.
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Affiliation(s)
- Thomas B Duguet
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Julien Soichot
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Rostyslav Kuzyakiv
- S3IT, University of Zurich, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lars Malmström
- S3IT, University of Zurich, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Institute for Computational Science, University of Zurich, Zurich, Switzerland.,Division of Infection Medicine, Lund University, Lund, Sweden
| | - Lucienne Tritten
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
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15
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Smythe AB, Holovachov O, Kocot KM. Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny. BMC Evol Biol 2019; 19:121. [PMID: 31195978 PMCID: PMC6567515 DOI: 10.1186/s12862-019-1444-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/27/2019] [Indexed: 11/18/2022] Open
Abstract
Background Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum. Results We supplemented publicly available data by sequencing transcriptomes of nine free-living nematodes and two important outgroups and conducted a phylum-wide phylogenomic analysis including a total of 108 nematodes. Analysis of a dataset generated using a conservative orthology inference strategy resulted in a matrix with a high proportion of missing data and moderate to weak support for branching within and placement of Enoplia. A less conservative orthology inference approach recovered more genes and resulted in higher support for the deepest splits within Nematoda, recovering Enoplia as the sister taxon to the rest of Nematoda. Relationships within major clades were similar to those found in previously published studies based on 18S rDNA. Conclusions Expanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites. Inclusion of more free-living nematodes in future phylogenomic analyses will allow a clearer understanding of many interesting aspects of nematode evolution, such as morphological and molecular adaptations to parasitism and whether nematodes originated in a marine or terrestrial environment. Electronic supplementary material The online version of this article (10.1186/s12862-019-1444-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ashleigh B Smythe
- Department of Biology, Virginia Military Institute, 301B Maury-Brooke Hall, Lexington, VA, 24450, USA
| | - Oleksandr Holovachov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05, Stockholm, Sweden
| | - Kevin M Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Campus Box 870344, Tuscaloosa, AL, 35487, USA.
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16
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Homan EJ, Bremel RD. A Role for Epitope Networking in Immunomodulation by Helminths. Front Immunol 2018; 9:1763. [PMID: 30108588 PMCID: PMC6079203 DOI: 10.3389/fimmu.2018.01763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
Helminth infections, by nematodes, trematodes, or cestodes, can lead to the modulation of host immune responses. This allows long-duration parasite infections and also impacts responses to co-infections. Surface, secreted, excreted, and shed proteins are thought to play a major role in modulation. A commonly reported feature of such immune modulation is the role of T regulatory (Treg) cells and IL-10. Efforts to identify helminth proteins, which cause immunomodulation, have identified candidates but not provided clarity as to a uniform mechanism driving modulation. In this study, we applied a bioinformatics systems approach, allowing us to analyze predicted T-cell epitopes of 17 helminth species and the responses to their surface proteins. In addition to major histocompatibility complex (MHC) binding, we analyzed amino acid motifs that would be recognized by T-cell receptors [T-cell-exposed motifs (TCEMs)]. All the helminth species examined have, within their surface proteins, peptides, which combine very common TCEMs with predicted high affinity binding to many human MHC alleles. This combination of features would result in large cognate T cell and a high probability of eliciting Treg responses. The TCEMs, which determine recognition by responding T-cell clones, are shared to a high degree between helminth species and with Plasmodium falciparum and Mycobacterium tuberculosis, both common co-infecting organisms. The implication of our observations is not only that Treg cells play a significant role in helminth-induced immune modulation but also that the epitope specificities of Treg responses are shared across species and genera of helminth. Hence, the immune response to a given helminth cannot be considered in isolation but rather forms part of an epitope ecosystem, or microenvironment, in which potentially immunosuppressive peptides in the helminth network via their common T-cell receptor recognition signals with T-cell epitopes in self proteins, microbiome, other helminths, and taxonomically unrelated pathogens. Such a systems approach provides a high-level view of the antigen-immune system signaling dynamics that may bias a host's immune response to helminth infections toward immune modulation. It may indicate how helminths have evolved to select for peptides that favor long-term parasite host coexistence.
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