Abstract
Intron retention (IR) refers to the mechanism of alternative splicing in which an intron is not excised from the mature transcript. IR in the cosmopolitan free-living amoeba Acanthamoeba castellanii has not been studied. We performed an analysis of RNA sequencing data during encystment to identify genes that presented differentially retained introns during this process. We show that IR increases during cyst formation, indicating a potential mechanism of gene regulation that could help downregulate metabolism. We identify 69 introns from 67 genes that are differentially retained comparing the trophozoite stage and encystment after 24 and 48 h. These genes include several hypothetical proteins. We show different patterns of IR during encystment taking as examples a lipase, a peroxin-3 protein, an Fbox domain containing protein, a proteasome subunit, a polynucleotide adenylyltransferase, and a tetratricopeptide domain containing protein. A better understanding of IR in Acanthamoeba, and even other protists, could help elucidate changes in life cycle and combat disease such as Acanthamoeba keratitis in which the cyst is key for its persistence.
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The information of the discussed genes can be found in the supplementary materials. Everything else can be provided upon request.
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Acknowledgements
We would like to thank Christian Q. Scheckhuber for proofreading and the positive feedback provided.
Funding
The study was supported by Mexico’s National Council of Science and Technology (CONACYT) and a University of Edinburgh College of Medicine and Veterinary Medicine PhD Studentship (to A. d. O. F. d. V.). Edinburgh Genomics is partly supported through core grants from NERC (R8/H10/56), MRC (MR/K001744/1), and BBSRC (BB/J004243/1).
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A. d. O. F. d. V conceived the study, isolated the strain, performed RNA-Seq, analyzed RNA expression and IR data, and wrote the first draft of the manuscript. J. G. M. planned and analyzed IR data and contributed intellectually to the paper. S. K. M. supervised the project, contributed intellectually, and edited the manuscript. All authors read and approved the final manuscript.
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Sutherland K. Maciver is part of the editorial board of Parasitology Research.
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de Obeso Fernández del Valle, A., Gómez-Montalvo, J. & Maciver, S.K. Acanthamoeba castellanii exhibits intron retention during encystment. Parasitol Res 121, 2615–2622 (2022). https://doi.org/10.1007/s00436-022-07578-5
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DOI: https://doi.org/10.1007/s00436-022-07578-5