Learning from the rDNA Operon: A Reanalysis of the Acanthamoeba palestinensis Group
Abstract
1. Introduction
2. Materials and Methods
3. Results
3.1. Sequence Identification by 18S rDNA Phylogeny
3.2. Partial LSU rDNA Analysis and Phylogeny
3.3. ITS Analysis and Phylogeny
3.4. ITS-2 Structure
4. Discussion
Funding
Data Availability Statement
Conflicts of Interest
References
- Marciano-Cabral, F.; Cabral, G. Acanthamoeba spp. as agents of disease in humans. Clin. Microbiol. Rev. 2003, 16, 273–307. [Google Scholar] [CrossRef] [PubMed]
- Stothard, D.R.; Schroeder-Diedrich, J.M.; Awwad, M.H.; Gast, R.J.; Ledee, D.R.; Rodriguez-Zaragoza, S.; Dean, C.L.; Fuerst, P.A.; Byers, T.J. The evolutionary history of the genus Acanthamoeba and the identification of eight new 18S rRNA gene sequence types. J. Eukaryot. Microbiol. 1998, 45, 45–54. [Google Scholar] [CrossRef] [PubMed]
- Corsaro, D. Update on Acanthamoeba phylogeny. Parasitol. Res. 2020, 119, 3327–3338. [Google Scholar] [CrossRef] [PubMed]
- Corsaro, D.; Venditti, D. Molecular evidence for a new lineage within the Acanthamoeba T4 genotype. Parasitol. Res. 2023, 122, 1445–1450. [Google Scholar] [CrossRef] [PubMed]
- Pussard, M.; Pons, R. Morphologie de la paroi kystique et taxonomie du genre Acanthamoeba (Protozoa, Amoebida). Protistologica 1977, 13, 557–598. [Google Scholar]
- Page, F.C. A New Key to Freshwater and Soil Gymnamoebae; Freshwater Biological Association: Ambleside, UK, 1988; pp. 92–97. [Google Scholar]
- Corsaro, D.; Mrva, M.; Colson, P.; Walochnik, J. Validation and redescription of Acanthamoeba terricola Pussard, 1964 (Amoebozoa: Acanthamoebidae). Eur. J. Protistol. 2024, 94, 126091. [Google Scholar] [CrossRef]
- Sonnenberg, R.; Nolte, A.W.; Tautz, D. An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Front. Zool. 2007, 4, 6. [Google Scholar] [CrossRef]
- Heeger, F.; Wurzbacher, C.; Bourne, E.C.; Mazzoni, C.J.; Monaghan, M.T. Combining the 5.8S and ITS2 to improve classification of fungi. Methods Ecol. Evol. 2019, 10, 1702–1711. [Google Scholar] [CrossRef]
- Corsaro, D. Exploring LSU and ITS rDNA sequences for Acanthamoeba identification and phylogeny. Microorganisms 2022, 10, 1776. [Google Scholar] [CrossRef]
- Page, F.C. Re-definition of the genus Acanthamoeba with description of three species. J. Protozool. 1967, 14, 709–724. [Google Scholar] [CrossRef]
- De Jonckheere, J.F. Isoenzyme and total protein analysis by agarose isoelectric focusing, and taxonomy of the genus Acanthamoeba. J. Protozool. 1983, 30, 701–706. [Google Scholar] [CrossRef]
- Corsaro, D.; Venditti, D. Phylogenetic evidence for a new genotype of Acanthamoeba (Amoebozoa, Acanthamoebida). Parasitol. Res. 2010, 107, 233–238. [Google Scholar] [CrossRef] [PubMed]
- Sawyer, T.K. The influence of seawater media on growth and encystment of Acanthamoeba polyphaga. Proc. Helminthol. Soc. Wash. 1970, 37, 182–188. [Google Scholar]
- Liu, H.; Ha, Y.-R.; Lee, S.-T.; Hong, Y.-C.; Kong, H.-H.; Chung, D.-I. Genetic diversity of Acanthamoeba isolated from ocean sediments. Korean J. Parasitol. 2006, 44, 117–125. [Google Scholar] [CrossRef] [PubMed]
- Walochnik, J.; Haller-Schober, E.; Kölli, H.; Picher, O.; Obwaller, A.; Aspöck, H. Discrimination between clinically relevant and nonrelevant Acanthamoeba strains isolated from contact lens-wearing keratitis patients in Austria. J. Clin. Microbiol. 2000, 38, 3932–3936. [Google Scholar] [CrossRef]
- Breiman, R.F.; Fields, B.S.; Sanden, G.N.; Volmer, L.; Meier, A.; Spika, J.S. Association of shower use with Legionnaires’ disease. Possible role of amoebae. JAMA 1990, 263, 2924–2926. [Google Scholar] [CrossRef]
- Amaral-Zettler, L.A.; Anderson, O.R.; Nerad, T.A.; Sogin, M.L. The phylogenetic position of Comandonia operculata and its implications for the taxonomy of the genus Acanthamoeba. In Proceedings of the IXth International Meeting on the Biology and Pathogenicity of Free-Living Amoebae Proceedings, Paris, France, 8–14 July 2001; Billot-Bonef, S., Cabanes, P.A., Marciano-Cabral, F., Pernin, P., Pringuez, E., Eds.; John Libbey Eurotext: Paris, France, 2001; pp. 235–242. [Google Scholar]
- Pernin, P.; Pussard, M. Étude en microscopie photonique et électronique d’une amibe voisine du genre Acanthamoeba: Comandonia operculata n. gen., n. sp. (Amoebida, Acanthamoebidae). Protistologica 1979, 15, 87–102. [Google Scholar]
- Kudryavtsev, A.; Wylezich, C.; Schlegel, M.; Walochnik, J.; Michel, R. Ultrastructure, SSU rRNA gene sequences and phylogenetic relationships of Flamella Schaeffer, 1926 (Amoebozoa), with description of three new species. Protist 2009, 160, 21–40. [Google Scholar] [CrossRef]
- Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef]
- Hall, T.A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic 369 Acids Symp. Ser. 1999, 41, 95–98. [Google Scholar]
- Corsaro, D.; Walochnik, J.; Köhsler, M.; Rott, M.B. Acanthamoeba misidentification and multiple labels: Redefining genotypes T16, T19 and T20, and proposal for Acanthamoeba micheli sp. nov. (genotype T19). Parasitol. Res. 2015, 114, 2481–2490. [Google Scholar] [CrossRef]
- Jobb, G.; von Haeseler, A.; Strimmer, K. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4, 18. [Google Scholar] [CrossRef] [PubMed]
- Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016, 33, 1870–1874. [Google Scholar] [CrossRef] [PubMed]
- Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406–3415. [Google Scholar] [CrossRef]
- Petrov, A.S.; Bernier, C.R.; Hershkovits, E.; Xue, Y.; Waterbury, C.C.; Hsiao, C.; Stepanov, V.G.; Gaucher, E.A.; Grover, M.A.; Harvey, S.C.; et al. Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res. 2013, 41, 7522–7535. [Google Scholar] [CrossRef] [PubMed]
- Stevens, A.R.; Pachler, P.F. Discontinuity of 26 s rRNA in Acanthamoeba castellani. J. Mol. Biol. 1972, 66, 225–237. [Google Scholar] [CrossRef]
- D’Alessio, J.M.; Harris, G.H.; Perna, P.J.; Paule, M.R. Ribosomal ribonucleic acid repeat unit of Acanthamoeba castellanii: Cloning and restriction endonuclease map. Biochemistry 1981, 20, 3822–3827. [Google Scholar] [CrossRef]
- Köhsler, M.; Leitner, B.; Blaschitz, M.; Michel, R.; Aspöck, H.; Walochnik, J. ITS1 sequence variabilities correlate with 18S rDNA sequence types in the genus Acanthamoeba (Protozoa: Amoebozoa). Parasitol. Res. 2006, 98, 86–93. [Google Scholar] [CrossRef]
- Maghsood, A.H.; Sissons, J.; Rezaian, M.; Nolder, D.; Warhurst, D.; Khan, N.A. Acanthamoeba genotype T4 from the UK and Iran and isolation of the T2 genotype from clinical isolates. J. Med. Microbiol. 2005, 54, 755–759. [Google Scholar] [CrossRef]
- Yera, H.; Zamfir, O.; Bourcier, T.; Ancelle, T.; Batellier, L.; Dupouy-Camet, J.; Chaumeil, C. Comparison of PCR, microscopic examination and culture for the early diagnosis and characterization of Acanthamoeba isolates from ocular infections. Eur. J. Clin. Microbiol. Infect. Dis. 2007, 26, 221–224. [Google Scholar] [CrossRef]
- Risler, A.; Coupat-Goutaland, B.; Pélandakis, M. Genotyping and phylogenetic analysis of Acanthamoeba isolates associated with keratitis. Parasitol. Res. 2013, 112, 3807–3816. [Google Scholar] [CrossRef] [PubMed]
- Jercic, M.I.; Aguayo, C.; Saldarriaga-Córdoba, M.; Muiño, L.; Chenet, S.M.; Lagos, J.; Osuna, A.; Fernández, J. Genotypic diversity of Acanthamoeba strains isolated from Chilean patients with Acanthamoeba keratitis. Parasit. Vectors 2019, 12, 58. [Google Scholar] [CrossRef] [PubMed]
- Holmgaard, D.B.; Barnadas, C.; Mirbarati, S.H.; O’Brien Andersen, L.; Nielsen, H.V.; Stensvold, C.R. Detection and Identification of Acanthamoeba and other nonviral causes of infectious keratitis in corneal scrapings by Real-Time PCR and Next-Generation Sequencing-Based 16S-18S gene analysis. J. Clin. Microbiol. 2021, 59, e02224-20. [Google Scholar] [CrossRef] [PubMed]
- Walochnik, J.; Aichelburg, A.; Assadian, O.; Steuer, A.; Visvesvara, G.; Vetter, N.; Aspöck, H. Granulomatous amoebic encephalitis caused by Acanthamoeba amoebae of genotype T2 in a human immunodeficiency virus-negative patient. J. Clin. Microbiol. 2008, 46, 338–340. [Google Scholar] [CrossRef] [PubMed]
- Kim, Y.H.; Ock, M.-S.; Yun, H.-C.; Hwang, M.Y.; Yu, H.-S.; Kong, H.-H.; Chung, D.-I. Close relatedness of Acanthamoeba pustulosa with Acanthamoeba palestinensis based on isoenzyme profiles and rDNA PCR-RFLP patterns. Korean J. Parasitol. 1996, 34, 259–266. [Google Scholar] [CrossRef]
- Müller, T.; Philippi, N.; Dandekar, T.; Schultz, J.; Wolf, M. Distinguishing species. RNA 2007, 13, 1469–1472. [Google Scholar] [CrossRef]
- Coleman, A.W. Pan-eukaryote ITS-2 homologies revealed by RNA secondary structure. Nucleic Acids Res. 2007, 35, 3322–3329. [Google Scholar] [CrossRef]
- Coleman, A.W. Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide. Mol. Phylogenet. Evol. 2009, 50, 197–203. [Google Scholar] [CrossRef]
GT | Species | Group | ITS2 Helix Length (nt) | ||||
---|---|---|---|---|---|---|---|
I | II | IIIa | III | IV | |||
T2 | A. palestinensis | Reich | 46 | 38 | 23 | 500 | – |
OX1 | Acanthamoeba sp. | (A) | 28 | 54 | 15–25 | 370–390 | – |
T6 | Acanthamoeba sp. | long (C) | 36–46 | 50 | 16–17 | 500–505 | – |
short (B) | 37–54 | 36–41 | – | 140 | – |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2024 by the author. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Corsaro, D. Learning from the rDNA Operon: A Reanalysis of the Acanthamoeba palestinensis Group. Microorganisms 2024, 12, 2105. https://doi.org/10.3390/microorganisms12102105
Corsaro D. Learning from the rDNA Operon: A Reanalysis of the Acanthamoeba palestinensis Group. Microorganisms. 2024; 12(10):2105. https://doi.org/10.3390/microorganisms12102105
Chicago/Turabian StyleCorsaro, Daniele. 2024. "Learning from the rDNA Operon: A Reanalysis of the Acanthamoeba palestinensis Group" Microorganisms 12, no. 10: 2105. https://doi.org/10.3390/microorganisms12102105
APA StyleCorsaro, D. (2024). Learning from the rDNA Operon: A Reanalysis of the Acanthamoeba palestinensis Group. Microorganisms, 12(10), 2105. https://doi.org/10.3390/microorganisms12102105