Structural definition of babesial RAP-1 proteins identifies a novel protein superfamily across Apicomplexa.


Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
15 Dec 2023
Historique:
received: 08 08 2023
accepted: 08 12 2023
medline: 16 12 2023
pubmed: 16 12 2023
entrez: 15 12 2023
Statut: epublish

Résumé

Apicomplexan protozoa are intracellular parasites of medical and economic importance. These parasites contain specialized apical complex organelles, including rhoptries, that participate in the process of host cell invasion. Conserved antigens expressed in the rhoptries are rational vaccine targets, but whether conservation of protein structure is a functional requirement for invasion remains unknown. Novel protein structural modeling enables identification of structurally conserved protein families that are not evident by sequence analysis alone. Here we show by AlphaFold2 structural modeling that the rhoptry-associated protein 1 superfamily of the Piroplasmida hemoparasites Babesia and Theileria (pRAP-1) is structurally conserved, with the core conserved region being composed of a globin-like and a 4-helix bundle subdomain. Search for structurally related members of this protein family in other apicomplexan parasites revealed structural homologues of pRAP-1 in several species of Plasmodium, Toxoplasma gondii and other members of the Sarcocystidae family. Based on these structural findings, pRAP-1 is a conserved apical complex protein, but whether these proteins share functional features in different species remains unknown. Identification of widely conserved elements involved in infection in these parasites will enhance our knowledge of invasion mechanisms, and facilitate the design of methods for controlling diseases that affect humans and animals globally.

Identifiants

pubmed: 38102310
doi: 10.1038/s41598-023-49532-0
pii: 10.1038/s41598-023-49532-0
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

22330

Subventions

Organisme : United States Department of Agriculture
ID : 2090- 32000-040-00-D

Informations de copyright

© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.

Références

Harding, C. R. & Frischknecht, F. The riveting cellular structures of apicomplexan parasites. Trends Parasitol. 36, 979–991 (2020).
doi: 10.1016/j.pt.2020.09.001 pubmed: 33011071
Florin-Christensen, M. et al. Pursuing effective vaccines against cattle diseases caused by apicomplexan protozoa. CABI Agric. Biosci. https://doi.org/10.1079/PAVSNNR202116024 (2021).
doi: 10.1079/PAVSNNR202116024
Chaabene, R. B., Lentini, G. & Soldati-Favre, D. Biogenesis and discharge of the rhoptries: Key organelles for entry and hijack of host cells by the Apicomplexa. Mol. Microbiol. 115(3), 453–465 (2020).
doi: 10.1111/mmi.14674
González, L. M. et al. Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes. PLoS Negl. Trop Dis. 13(8), e0007680. https://doi.org/10.1371/journal.pntd.0007680.eCollection (2019).
doi: 10.1371/journal.pntd.0007680.eCollection pubmed: 31425518 pmcid: 6715253
Gohil, S., Kats, L. M., Sturm, A. & Cooke, B. M. Recent insights into alteration of red blood cells by Babesia bovis: Moovin’ forward. Trends Parasitol. 26, 591–599 (2010).
doi: 10.1016/j.pt.2010.06.012 pubmed: 20598944
Asada, M. et al. Gliding motility of Babesia bovis merozoites visualized by time-lapse video microscopy. PLoS One 7(4), e35227. https://doi.org/10.1371/journal.pone.0035227 (2012).
doi: 10.1371/journal.pone.0035227 pubmed: 22506073 pmcid: 3323635
Bastos, R. G. et al. Babesia microti Immunoreactive Rhoptry-Associated Protein-1 Paralogs Are Ancestral Members of the Piroplasmid-Confined RAP-1 Family. Pathogens 10(11), 1384. https://doi.org/10.3390/pathogens10111384 (2021).
doi: 10.3390/pathogens10111384 pubmed: 34832541 pmcid: 8624774
Suarez, C. E. et al. A novel neutralization sensitive and subdominant RAP-1-related antigen (RRA) is expressed by Babesia bovis merozoites. Parasitology 138(7), 809–818. https://doi.org/10.1017/S0031182011000321 (2011).
doi: 10.1017/S0031182011000321 pubmed: 21554842
Suarez, C. E., McElwain, T. F., Stephens, E. B., Mishra, V. S. & Palmer, G. H. Sequence conservation among merozoite apical complex proteins of Babesia bovis, Babesia bigemina and other apicomplexa. Mol. Biochem. Parasitol. 49(2), 329–332. https://doi.org/10.1016/0166-6851(91)90077-j (1991).
doi: 10.1016/0166-6851(91)90077-j pubmed: 1775174
Yokoyama, N. et al. Cellular localization of Babesia bovis merozoite rhoptry-associated protein 1 and its erythrocyte-binding activity. Infect Immun. 70(10), 5822–5826. https://doi.org/10.1128/IAI.70.10.5822-5826 (2002).
doi: 10.1128/IAI.70.10.5822-5826 pubmed: 12228313 pmcid: 128354
Brown, W. C. et al. Babesia bovis rhoptry-associated protein 1 is immunodominant for T helper cells of immune cattle and contains T-cell epitopes conserved among geographically distant B. bovis strains. Infect Immun. 64(8), 3341–50. https://doi.org/10.1128/iai.64.8.3341-3350.1996 (1996).
doi: 10.1128/iai.64.8.3341-3350.1996 pubmed: 8757873 pmcid: 174227
Suarez, C. E., Palmer, G. H., Hötzel, I. & McElwain, T. F. Structure, sequence, and transcriptional analysis of the Babesia bovis rap-1 multigene locus. Mol. Biochem. Parasitol. 93(2), 215–24 (1998).
pubmed: 9662706
Suarez, C. E., Palmer, G. H., Hines, S. A. & McElwain, T. F. Immunogenic B-cell epitopes of Babesia bovis rhoptry-associated protein 1 are distinct from sequences conserved between species. Infect Immun. 61(8), 3511–3517. https://doi.org/10.1128/iai.61.8.3511-3517.1993 (1993).
doi: 10.1128/iai.61.8.3511-3517.1993 pubmed: 7687587 pmcid: 281030
Suarez, C. E. et al. Organization, transcription, and expression of rhoptry associated protein genes in the Babesia bigemina rap-1 locus. Mol. Biochem. Parasitol. 127(2), 101–112. https://doi.org/10.1016/s0166-6851(02)00311-0 (2003).
doi: 10.1016/s0166-6851(02)00311-0 pubmed: 12672519
Onzere, C. K. et al. Theileria equi RAP-1a and RAP-1b proteins contain immunoreactive epitopes and are suitable candidates for vaccine and diagnostics development. Int. J. Parasitol. 52(6), 385–397. https://doi.org/10.1016/j.ijpara.2022.01.004 (2022).
doi: 10.1016/j.ijpara.2022.01.004 pubmed: 35318949
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589. https://doi.org/10.1038/s41586-021-03819-2 (2021).
doi: 10.1038/s41586-021-03819-2 pubmed: 34265844 pmcid: 8371605
Tunyasuvunakool, K. et al. Highly accurate protein structure prediction for the human proteome. Nature 596, 590–596. https://doi.org/10.1038/s41586-021-03828-1 (2021).
doi: 10.1038/s41586-021-03828-1 pubmed: 34293799 pmcid: 8387240
Mirdita, M. et al. ColabFold: Making protein folding accessible to all. Nat. Methods 19(6), 679–682. https://doi.org/10.1038/s41592-022-01488-1 (2022).
doi: 10.1038/s41592-022-01488-1 pubmed: 35637307 pmcid: 9184281
Varadi, M. et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50(D1), D439–D444. https://doi.org/10.1093/nar/gkab1061 (2022).
doi: 10.1093/nar/gkab1061 pubmed: 34791371
Suarez, C. E., Thompson, S. M., McElwain, T. F., Hines, S. A. & Palmer, G. H. Conservation of oligopeptide motifs in rhoptry proteins from different genera of erythroparasitic protozoa. Exp. Parasitol. 78(2), 246–251. https://doi.org/10.1006/expr.1994.1025 (1994).
doi: 10.1006/expr.1994.1025 pubmed: 8119378
Holm, L. DALI and the persistence of protein shape. Protein Sci. 29, 128–140. https://doi.org/10.1002/pro.3749 (2020).
doi: 10.1002/pro.3749 pubmed: 31606894
Zheng, W. et al. Identification of three ookinete-specific genes and evaluation of their transmission-blocking potentials in Plasmodium berghei. Vaccine 34(23), 2570–2578. https://doi.org/10.1016/j.vaccine.2016.04.011 (2016).
doi: 10.1016/j.vaccine.2016.04.011 pubmed: 27083421 pmcid: 4864593
Ukegbu, C. V., Christophides, G. K. & Vlachou, D. Identification of three novel plasmodium factors involved in ookinete to oocyst developmental transition. Front. Cell Infect. Microbiol. 11, 634273. https://doi.org/10.3389/fcimb.2021.634273 (2021).
doi: 10.3389/fcimb.2021.634273 pubmed: 33791240 pmcid: 8005625
Hassabis, D. & Velankar, S. AlphaFold Protein Structure Database: Massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50(D1), D439–D444. https://doi.org/10.1093/nar/gkab1061 (2022).
doi: 10.1093/nar/gkab1061 pubmed: 34791371
van Kempen, M. et al. Foldseek: fast and accurate protein structure search. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01773-0 (2023).
doi: 10.1038/s41587-023-01773-0 pubmed: 37156916
Hou, S. et al. Globin-coupled sensors: A class of heme-containing sensors in Archaea and Bacteria. Proc. Natl. Acad. Sci. U S A. 98(16), 9353–9358. https://doi.org/10.1073/pnas.161185598 (2001).
doi: 10.1073/pnas.161185598 pubmed: 11481493 pmcid: 55424
Suarez, C. E. & McElwain, T. F. Stable expression of a GFP-BSD fusion protein in Babesia bovis merozoites. Int. J. Parasitol. 39(3), 289–297. https://doi.org/10.1016/j.ijpara.2008.08.006 (2009).
doi: 10.1016/j.ijpara.2008.08.006 pubmed: 18831975
Hakimi, H. et al. Genome editing of Babesia bovis using the CRISPR/Cas9 system. mSphere 4(3), e00109. https://doi.org/10.1128/mSphere.00109-19 (2019).
doi: 10.1128/mSphere.00109-19 pubmed: 31189559 pmcid: 6563353
Etheridge, R. D. et al. The Toxoplasma pseudokinase ROP5 forms complexes with ROP18 and ROP17 kinases that synergize to control acute virulence in mice. Cell Host Microbe. 15(5), 537–550. https://doi.org/10.1016/j.chom.2014.04.002 (2014).
doi: 10.1016/j.chom.2014.04.002 pubmed: 24832449 pmcid: 4086214

Auteurs

Isidro Hötzel (I)

Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA.

Carlos E Suarez (CE)

Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA. carlos.suarez@usda.gov.
Animal Disease Research Unit, United States Department of Agriculture - Agricultural Research Service, Pullman, WA, USA. carlos.suarez@usda.gov.

Classifications MeSH