TY - JOUR

T1 - RNA-seq analysis of parasitism by Intoshia linei (Orthonectida) reveals protein effectors of defence, communication, feeding and growth

AU - Skalon, Elizaveta K.

AU - Starunov, Viktor V.

AU - Slyusarev, George S.

N1 - Export Date: 4 March 2024 Адрес для корреспонденции: Skalon, E.K.; Department of Invertebrate Zoology, Russian Federation; эл. почта: elizavetaskalon@gmail.com Сведения о финансировании: Russian Science Foundation, RSF, 23‐24‐00193 Текст о финансировании 1: We are thankful to Dr. M. Makarov for providing accommodation and facilities for field work at the Barents Sea and to the staff of the Marine Biological Station of Saint Petersburg State University for the assistance in collecting the material. Sincere thanks are extended to N. I. Abramson and the staff of the Laboratory of Evolutionary Genomics and Paleogenomics (Zoological Institute RAS) for their insightful comments. The study was performed at the Resource Centers for Microscopy and Microanalysis, Molecular and Cell Technologies, “CHROMAS,” “Culture Collection of Microorganisms” and “Biobank” of St Petersburg State University and ICG SB RAS “Bioinformatics” Core Facility. Financial support for this study was provided by the Russian Science Foundation grant № 23‐24‐00193 to G.S.S. Пристатейные ссылки: Americus, B., Hams, N., Klompen, A.M.L., Alama-Bermejo, G., Lotan, T., Bartholomew, J.L., Atkinson, S.D., The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection (2021) PeerJ, 9. , https://doi.org/10.7717/peerj.12606; Anders, S., Huber, W., Differential expression analysis for sequence count data (2010) Genome Biology, 11. , https://doi.org/10.1186/gb-2010-11-10-r106; Andreu, Z., Yáñez-Mó, M., Tetraspanins in extracellular vesicle formation and function (2014) Frontiers in Immunology, 5. , https://doi.org/10.3389/fimmu.2014.00442; Bondarenko, N., Bondarenko, A., Starunov, V., Slyusarev, G., Comparative analysis of the mitochondrial genomes of Orthonectida: Insights into the evolution of an invertebrate parasite species (2019) Molecular Genetics and Genomics, 294 (3), pp. 715-727. , https://doi.org/10.1007/s00438-019-01543-1; Campos, T.D.L., Young, N.D., Korhonen, P.K., Hall, R.S., Mangiola, S., Lonie, A., Gasser, R.B., Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics (2014) Parasites & Vectors, 7. , https://doi.org/10.1186/1756-3305-7-242; Caullery, M., Classe des Orthonectides (Orthonectida Giard 1877) (1961) Traité de Zoologie, IV, pp. 695-706; Chaiyadet, S., Sotillo, J., Krueajampa, W., Thongsen, S., Smout, M., Brindley, P.J., Laha, T., Loukas, A., Silencing of Opisthorchis viverrini tetraspanin gene expression results in reduced secretion of extracellular vesicles (2022) Frontiers in Cellular and Infection Microbiology, 12. , https://doi.org/10.3389/fcimb.2022.827521; Coakley, G., Maizels, R.M., Buck, A.H., Exosomes and other extracellular vesicles: The new communicators in parasite infections (2015) Trends in Parasitology, 31 (10), pp. 477-489. , https://doi.org/10.1016/j.pt.2015.06.009; Drábková, M., Kocot, K.M., Halanych, K.M., Oakley, T.H., Moroz, L.L., Cannon, J.T., Kuris, A., Zrzavý, J., Different phylogenomic methods support monophyly of enigmatic “Mesozoa” (Dicyemida + Orthonectida, Lophotrochozoa) (2022) Proceedings of the Royal Society B: Biological Sciences, 289 (1978). , https://doi.org/10.1098/rspb.2022.0683; Drurey, C., Maizels, R.M., Helminth extracellular vesicles: Interactions with the host immune system (2021) Molecular Immunology, 137, pp. 124-133. , https://doi.org/10.1016/j.molimm.2021.06.017; Espindula, E., Sperb, E.R., Bach, E., Passaglia, L.M.P., The combined analysis as the best strategy for dual RNA-seq mapping (2019) Genetics and Molecular Biology, 42 (4). , https://doi.org/10.1590/1678-4685-GMB-2019-0215; Giard, A., Sur les Orthonectida, classe nouvelle d'animaux parasites des Echinodermes et des Turbellariés (1877) Comptes Rendus Des Séances de l'Académie Des Sciences, 85, pp. 812-814; Groat-Carmona, A.M., Kain, H., Brownell, J., Douglass, A.N., Aly, A.S.I., Kappe, S.H.I., A plasmodium α/β-hydrolase modulates the development of invasive stages (2015) Cellular Microbiology, 17, pp. 1848-1867. , https://doi.org/10.1111/cmi.12477; Gurung, S., Perocheau, D., Touramanidou, L., Baruteau, J., The exosome journey: From biogenesis to uptake and intracellular signalling (2021) Cell Communication and Signaling, 19 (1), p. 47. , https://doi.org/10.1186/s12964-021-00730-1; Khalturin, K., Hemmrich, G., Fraune, S., Augustin, R., Bosch, T.C.G., More than just orphans: Are taxonomically-restricted genes important in evolution? (2009) Trends in Genetics. Trends Genet, 25 (9), pp. 404-413. , https://doi.org/10.1016/j.tig.2009.07.006; Kozloff, E.N., The structure and origin of the plasmodium of Rhopalura ophiocomae (Phylum Orthonectida) (1994) Acta Zoologica, 75, pp. 191-199. , https://doi.org/10.1111/j.1463-6395.1994.tb01206.x; Kozloff, E.N., Studies on the so-called plasmodium of Ciliocincta sabellariae (Phylum Orthonectida), with notes on an associated microsporan parasite (1997) Cahiers de Biologie Marine, 38, pp. 151-159; Kumari, S., Mg, S., Mayor, S., Endocytosis unplugged: Multiple ways to enter the cell (2010) Cell Research, 20 (3), pp. 256-275. , https://doi.org/10.1038/cr.2010.19; Laing, R., Kikuchi, T., Martinelli, A., Tsai, I.J., Beech, R.N., Redman, E., Holroyd, N., Cotton, J.A., The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery (2013) Genome Biology, 14. , https://doi.org/10.1186/gb-2013-14-8-r88; Liu, Y., Zhou, J., White, K.P., RNA-seq differential expression studies: More sequence or more replication? (2014) Bioinformatics, 30, pp. 301-304. , https://doi.org/10.1093/bioinformatics/btt688; Lu, M., Tian, X., Tian, A.-L., Li, C., Yan, R., Xu, L., Song, X., Li, X., A novel α/β hydrolase domain protein derived from Haemonchus contortus acts at the parasite-host interface (2020) Frontiers in immunology, 11. , https://doi.org/10.3389/fimmu.2020.01388; Lu, T.M., Kanda, M., Satoh, N., Furuya, H., The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution (2017) Zoological Letters, 3, p. 6. , https://doi.org/10.1186/s40851-017-0068-5; Maizels, R.M., Smits, H.H., McSorley, H.J., Modulation of host immunity by helminths: The expanding repertoire of parasite effector molecules (2018) Immunity Cell Press, 49 (5), pp. 801-818. , https://doi.org/10.1016/j.immuni.2018.10.016; Marcilla, A., Martin-Jaular, L., Trelis, M., de Menezes-Neto, A., Osuna, A., Bernal, D., Fernandez-Becerra, C., del Portillo, H.A., Extracellular vesicles in parasitic diseases (2014) Journal of Extracellular Vesicles, 3 (1). , https://doi.org/10.3402/jev.v3.25040; Marcilla, A., Pérez-García, A., Espert, A., Bernal, D., Muñoz-Antolí, C., Esteban, J.G., Toledo, R., Echinostoma caproni: Identification of enolase in excretory/secretory products, molecular cloning, and functional expression (2007) Experimental Parasitology, 117, pp. 57-64. , https://doi.org/10.1016/j.exppara.2007.03.011; Marcilla, A., Trelis, M., Cortés, A., Sotillo, J., Cantalapiedra, F., Minguez, M.T., Valero, M.L., Bernal, D., Extracellular vesicles from parasitic helminths contain specific excretory/secretory proteins and are internalized in intestinal host cells (2012) PLoS One, 7. , https://doi.org/10.1371/journal.pone.0045974; Mikhailov, K.V., Slyusarev, G.S., Nikitin, M.A., Logacheva, M.D., Penin, A.A., Aleoshin, V.V., Panchin, Y.V., The genome of Intoshia linei affirms orthonectids as highly simplified spiralians (2016) Current Biology, 26, pp. 1768-1774. , https://doi.org/10.1016/j.cub.2016.05.007; Montaner, S., Galiano, A., Trelis, M., Martin-Jaular, L., del Portillo, H.A., Bernal, D., Marcilla, A., The role of extracellular vesicles in modulating the host immune response during parasitic infections (2014) Frontiers in Immunology, 5. , https://doi.org/10.3389/fimmu.2014.00433; Nawaz, M., Malik, M.I., Hameed, M., Zhou, J., Research progress on the composition and function of parasite-derived exosomes (2019) Acta Tropica, 196, pp. 30-36. , https://doi.org/10.1016/j.actatropica.2019.05.004; O'Keeffe, K.R., Jones, C.D., Challenges and solutions for analysing dual RNA-seq data for non-model host–pathogen systems (2019) Methods in Ecology and Evolution, 10 (3), pp. 401-414. , https://doi.org/10.1111/2041-210X.13135; Orús-Alcalde, A., Børve, A., Hejnol, A., The localization of Toll and Imd pathway and complement system components and their response to Vibrio infection in the nemertean Lineus ruber (2023) BMC Biology, 21, p. 7. , https://doi.org/10.1186/s12915-022-01482-1; Pees, B., Yang, W., Zárate-Potes, A., Schulenburg, H., Dierking, K., High innate immune specificity through diversified C-Type Lectin-Like domain proteins in invertebrates (2016) Journal of Innate Immunity, 8, pp. 129-142. , https://doi.org/10.1159/000441475; Poulin, R., The many roads to parasitism. A tale of convergence (2011) Advances in parasitology, 74, pp. 1-40. , https://doi.org/10.1016/B978-0-12-385897-9.00001-X; Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C.E., Betel, D., Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data (2013) Genome Biology, 14. , https://doi.org/10.1186/gb-2013-14-9-r95; Schiffer, P.H., Robertson, H.E., Telford, M.J., Orthonectids are highly degenerate annelid worms (2018) Current Biology, 28, pp. 1970-1974.e3. , https://doi.org/10.1016/j.cub.2018.04.088; Schulenburg, H., Hoeppner, M.P., Weiner, J., Bornberg-Bauer, E., Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans (2008) Immunobiology, 213, pp. 237-250. , https://doi.org/10.1016/j.imbio.2007.12.004; Schwarz, E.M., Hu, Y., Antoshechkin, I., Miller, M.M., Sternberg, P.W., Aroian, R.V., The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families (2015) Nature Genetics, 47, pp. 416-422. , https://doi.org/10.1038/ng.3237; Skalon, E.K., Starunov, V.V., Bondarenko, N.I., Slyusarev, G.S., Plasmodium structure of Intoshia linei (Orthonectida) (2023) Journal of Morphology, 284. , https://doi.org/10.1002/jmor.21602; Slyusarev, G., Orthonectida (2018) Handbook of zoology: Miscellaneous invertebrates, , https://www.nhbs.com/handbook-of-zoology-miscellaneous-invertebrates, A. Schmidt-Rhaesa, (Ed.),, NHBS Academic & Professional Books; Slyusarev, G.S., Bondarenko, N.I., Skalon, E.K., Rappoport, A.K., Radchenko, D., Starunov, V.V., The structure of the muscular and nervous systems of the orthonectid Rhopalura litoralis (Orthonectida) or what parasitism can do to an annelid (2022) Organisms Diversity & Evolution, 22, pp. 35-45. , https://doi.org/10.1007/s13127-021-00519-7; Slyusarev, G.S., Cherkasov, A.S., Structure and supposed feeding mechanisms of the plasmodium of Intoshia linei (Orthonectida) (2009) Invertebrate Zoology, 5, pp. 47-51. , https://doi.org/10.15298/invertzool.05.1.05; Slyusarev, G.S., Miller, D.M., Fine structure of the mature plasmodium of Intoshia variabili (Phylum Orthonectida), a parasite of the platyhelminth Macrorhynchus crocea (1998) Acta Zoologica, 79, pp. 319-327. , https://doi.org/10.1111/j.1463-6395.1998.tb01281.x; Slyusarev, G.S., Nesterenko, M.A., Starunov, V.V., The structure of the muscular and nervous systems of the male Intoshia linei (Orthonectida) (2019) Acta Zoologica, 100, pp. 451-458. , https://doi.org/10.1111/azo.12279; Slyusarev, G.S., Skalon, E.K., Starunov, V.V., Evolution of Orthonectida body plan (2023) Evolution & Development; Slyusarev, G.S., Starunov, V.V., The structure of the muscular and nervous systems of the female Intoshia linei (Orthonectida) (2016) Organisms Diversity & Evolution, 16, pp. 65-71. , https://doi.org/10.1007/s13127-015-0246-2; Slyusarev, G.S., Starunov, V.V., Bondarenko, A.S., Zorina, N.A., Bondarenko, N.I., Extreme genome and nervous system streamlining in the invertebrate parasite Intoshia variabili (2020) Current Biology, 30, pp. 1292-1298.e3. , https://doi.org/10.1016/j.cub.2020.01.061; Viney, M., The genomic basis of nematode parasitism (2018) Briefings in Functional Genomics, 17 (7), pp. 8-14. , https://doi.org/10.1093/bfgp/elx010; Yang, Y., Xiong, J., Zhou, Z., Huo, F., Miao, W., Ran, C., Liu, Y., Yao, B., The genome of the myxosporean Thelohanellus kitauei shows adaptations to nutrient acquisition within its fish host (2014) Genome Biology and Evolution, 6, pp. 3182-3198. , https://doi.org/10.1093/gbe/evu247; Zarowiecki, M., Berriman, M., What helminth genomes have taught us about parasite evolution (2015) Parasitology, 142, pp. S85-9785. , https://doi.org/10.1017/S0031182014001449; Zverkov, O.A., Mikhailov, K.V., Isaev, S.V., Rusin, L.Y., Popova, O.V., Logacheva, M.D., Penin, A.A., Aleoshin, V.V., Dicyemida and Orthonectida: Two stories of body plan simplification (2019) Frontiers in Genetics, 10. , https://doi.org/10.3389/fgene.2019.00443

PY - 2024/7/1

Y1 - 2024/7/1

N2 - 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. © 2024 Wiley Periodicals LLC.

AB - 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. © 2024 Wiley Periodicals LLC.

KW - Intoshia linei

KW - Lineus ruber

KW - orthonectid plasmodium

KW - Orthonectida

KW - transcriptomics

UR - https://www.mendeley.com/catalogue/0cf90598-96d9-3dbf-98fb-ab9118494a99/

U2 - 10.1002/jez.b.23247

DO - 10.1002/jez.b.23247

M3 - статья

VL - 342

SP - 398

EP - 405

JO - Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

JF - Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

SN - 1552-5007

IS - 5

ER -