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Ballmer D, Carter W, van Hooff JJE, Tromer EC, Ishii M, Ludzia P, Akiyoshi B. Kinetoplastid kinetochore proteins KKT14-KKT15 are divergent Bub1/BubR1-Bub3 proteins. Open Biol 2024; 14:240025. [PMID: 38862021 DOI: 10.1098/rsob.240025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/12/2024] [Indexed: 06/13/2024] Open
Abstract
Faithful transmission of genetic material is crucial for the survival of all organisms. In many eukaryotes, a feedback control mechanism called the spindle checkpoint ensures chromosome segregation fidelity by delaying cell cycle progression until all chromosomes achieve proper attachment to the mitotic spindle. Kinetochores are the macromolecular complexes that act as the interface between chromosomes and spindle microtubules. While most eukaryotes have canonical kinetochore proteins that are widely conserved, kinetoplastids such as Trypanosoma brucei have a seemingly unique set of kinetochore proteins including KKT1-25. It remains poorly understood how kinetoplastids regulate cell cycle progression or ensure chromosome segregation fidelity. Here, we report a crystal structure of the C-terminal domain of KKT14 from Apiculatamorpha spiralis and uncover that it is a pseudokinase. Its structure is most similar to the kinase domain of a spindle checkpoint protein Bub1. In addition, KKT14 has a putative ABBA motif that is present in Bub1 and its paralogue BubR1. We also find that the N-terminal part of KKT14 interacts with KKT15, whose WD40 repeat beta-propeller is phylogenetically closely related to a direct interactor of Bub1/BubR1 called Bub3. Our findings indicate that KKT14-KKT15 are divergent orthologues of Bub1/BubR1-Bub3, which promote accurate chromosome segregation in trypanosomes.
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Affiliation(s)
- Daniel Ballmer
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, UK
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh , Edinburgh EH9 3BF, UK
| | - William Carter
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, UK
| | - Jolien J E van Hooff
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research , 6708 HB Wageningen, The Netherlands
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen , 9747 AG Groningen, The Netherlands
| | - Midori Ishii
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, UK
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh , Edinburgh EH9 3BF, UK
| | - Patryk Ludzia
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford , Oxford OX1 3QU, UK
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh , Edinburgh EH9 3BF, UK
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2
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Old Methods, New Insights: Reviewing Concepts on the Ecology of Trypanosomatids and Bodo sp. by Improving Conventional Diagnostic Tools. Pathogens 2023; 12:pathogens12010071. [PMID: 36678419 PMCID: PMC9864408 DOI: 10.3390/pathogens12010071] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
Mixed infections by different Trypanosoma species or genotypes are a common and puzzling phenomenon. Therefore, it is critical to refine the diagnostic techniques and to understand to what extent these methods detect trypanosomes. We aimed to develop an accessible strategy to enhance the sensitivity of the hemoculture, as well as to understand the limitations of the hemoculture and the blood clot as a source of parasitic DNA. We investigated trypanosomatid infections in 472 bats by molecular characterization (18S rDNA gene) of the DNA obtained from the blood clot and, innovatively, from three hemoculture sample types: the amplified flagellates ("isolate"), the pellet of the culture harvested in its very initial growth stage ("first aliquot"), and the pellet of non-grown cultures with failure of amplification ("sediment"). We compared (a) the characterization of the flagellates obtained by first aliquots and isolates; and (b) the performance of the hemoculture and blood clot for trypanosomatid detection. We observed: (i) a putative new species of Bodo in Artibeus lituratus; (ii) the potential of Trypanosoma cruzi selection in the hemoculture; (iii) that the first aliquots and sediments overcome the selective pressure of the hemoculture; and (iv) that the blood clot technique performs better than the hemoculture. However, combining these methods enhances the detection of single and mixed infections.
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Ishii M, Ludzia P, Marcianò G, Allen W, Nerusheva OO, Akiyoshi B. Divergent polo boxes in KKT2 bind KKT1 to initiate the kinetochore assembly cascade in Trypanosoma brucei. Mol Biol Cell 2022; 33:ar143. [PMID: 36129769 PMCID: PMC9727816 DOI: 10.1091/mbc.e22-07-0269-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 02/04/2023] Open
Abstract
Chromosome segregation requires assembly of the macromolecular kinetochore complex onto centromeric DNA. While most eukaryotes have canonical kinetochore proteins that are widely conserved among eukaryotes, evolutionarily divergent kinetoplastids have a unique set of kinetochore proteins. Little is known about the mechanism of kinetochore assembly in kinetoplastids. Here we characterize two homologous kinetoplastid kinetochore proteins, KKT2 and KKT3, that constitutively localize at centromeres. They have three domains that are highly conserved among kinetoplastids: an N-terminal kinase domain of unknown function, the centromere localization domain in the middle, and the C-terminal domain that has weak similarity to polo boxes of Polo-like kinases. We show that the kinase activity of KKT2 is essential for accurate chromosome segregation, while that of KKT3 is dispensable for cell growth in Trypanosoma brucei. Crystal structures of their divergent polo boxes reveal differences between KKT2 and KKT3. We also show that the divergent polo boxes of KKT3 are sufficient to recruit KKT2 in trypanosomes. Furthermore, we demonstrate that the divergent polo boxes of KKT2 interact directly with KKT1 and that KKT1 interacts with KKT6. These results show that the divergent polo boxes of KKT2 and KKT3 are protein-protein interaction domains that initiate kinetochore assembly in T. brucei.
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Affiliation(s)
- Midori Ishii
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Patryk Ludzia
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Gabriele Marcianò
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - William Allen
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Olga O. Nerusheva
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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4
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Mitochondrial RNA editing in Trypanoplasma borreli: new tools, new revelations. Comput Struct Biotechnol J 2022; 20:6388-6402. [DOI: 10.1016/j.csbj.2022.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
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5
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Hałakuc P, Karnkowska A, Milanowski R. Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans. BMC Ecol Evol 2022; 22:59. [PMID: 35534840 PMCID: PMC9082867 DOI: 10.1186/s12862-022-02014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
Background Members of Euglenozoa (Discoba) are known for unorthodox rDNA organization. In Euglenida rDNA is located on extrachromosomal circular DNA. In Kinetoplastea and Euglenida the core of the large ribosomal subunit, typically formed by the 28S rRNA, consists of several smaller rRNAs. They are the result of the presence of additional internal transcribed spacers (ITSs) in the rDNA. Diplonemea is the third of the main groups of Euglenozoa and its members are known to be among the most abundant and diverse protists in the oceans. Despite that, the rRNA of only one diplonemid species, Diplonema papillatum, has been examined so far and found to exhibit continuous 28S rRNA. Currently, the rDNA organization has not been researched for any diplonemid. Herein we investigate the structure of rRNA genes in classical (Diplonemidae) and deep-sea diplonemids (Eupelagonemidae), representing the majority of known diplonemid diversity. The results fill the gap in knowledge about diplonemid rDNA and allow better understanding of the evolution of the fragmented structure of the rDNA in Euglenozoa. Results We used available genomic (culture and single-cell) sequencing data to assemble complete or almost complete rRNA operons for three classical and six deep-sea diplonemids. The rDNA sequences acquired for several euglenids and kinetoplastids were used to provide the background for the analysis. In all nine diplonemids, 28S rRNA seems to be contiguous, with no additional ITSs detected. Similarly, no additional ITSs were detected in basal prokinetoplastids. However, we identified five additional ITSs in the 28S rRNA of all analysed metakinetoplastids, and up to twelve in euglenids. Only three of these share positions, and they cannot be traced back to their common ancestor. Conclusions Presented results indicate that independent origin of additional ITSs in euglenids and kinetoplastids seems to be the most likely. The reason for such unmatched fragmentation remains unknown, but for some reason euglenozoan ribosomes appear to be prone to 28S rRNA fragmentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02014-9.
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Ralton JE, Sernee MF, McConville MJ. Evolution and function of carbohydrate reserve biosynthesis in parasitic protists. Trends Parasitol 2021; 37:988-1001. [PMID: 34266735 DOI: 10.1016/j.pt.2021.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/28/2022]
Abstract
Nearly all eukaryotic cells synthesize carbohydrate reserves, such as glycogen, starch, or low-molecular-weight oligosaccharides. However, a number of parasitic protists have lost this capacity while others have lost, and subsequently evolved, entirely new pathways. Recent studies suggest that retention, loss, or acquisition of these pathways in different protists is intimately linked to their lifestyle. In particular, parasites with carbohydrate reserves often establish long-lived chronic infections and/or produce environmental cysts, whereas loss of these pathways is associated with parasites that have highly proliferative and metabolically active life-cycle stages. The evolution of mannogen biosynthesis in Leishmania and related parasites indicates that these pathways have played a role in defining the host range and niches occupied by some protists.
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Affiliation(s)
- Julie E Ralton
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia
| | - M Fleur Sernee
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Pharmacology, University of Melbourne, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria 3010, Australia.
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Marcianò G, Ishii M, Nerusheva OO, Akiyoshi B. Kinetoplastid kinetochore proteins KKT2 and KKT3 have unique centromere localization domains. J Cell Biol 2021; 220:212224. [PMID: 34081090 PMCID: PMC8178753 DOI: 10.1083/jcb.202101022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/29/2021] [Accepted: 05/12/2021] [Indexed: 12/31/2022] Open
Abstract
The kinetochore is the macromolecular protein complex that assembles onto centromeric DNA and binds spindle microtubules. Evolutionarily divergent kinetoplastids have an unconventional set of kinetochore proteins. It remains unknown how kinetochores assemble at centromeres in these organisms. Here, we characterize KKT2 and KKT3 in the kinetoplastid parasite Trypanosoma brucei. In addition to the N-terminal kinase domain and C-terminal divergent polo boxes, these proteins have a central domain of unknown function. We show that KKT2 and KKT3 are important for the localization of several kinetochore proteins and that their central domains are sufficient for centromere localization. Crystal structures of the KKT2 central domain from two divergent kinetoplastids reveal a unique zinc-binding domain (termed the CL domain for centromere localization), which promotes its kinetochore localization in T. brucei. Mutations in the equivalent domain in KKT3 abolish its kinetochore localization and function. Our work shows that the unique central domains play a critical role in mediating the centromere localization of KKT2 and KKT3.
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Affiliation(s)
| | - Midori Ishii
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
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8
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Tromer EC, Wemyss TA, Ludzia P, Waller RF, Akiyoshi B. Repurposing of synaptonemal complex proteins for kinetochores in Kinetoplastida. Open Biol 2021; 11:210049. [PMID: 34006126 PMCID: PMC8131943 DOI: 10.1098/rsob.210049] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Chromosome segregation in eukaryotes is driven by the kinetochore, a macromolecular complex that connects centromeric DNA to microtubules of the spindle apparatus. Kinetochores in well-studied model eukaryotes consist of a core set of proteins that are broadly conserved among distant eukaryotic phyla. By contrast, unicellular flagellates of the class Kinetoplastida have a unique set of 36 kinetochore components. The evolutionary origin and history of these kinetochores remain unknown. Here, we report evidence of homology between axial element components of the synaptonemal complex and three kinetoplastid kinetochore proteins KKT16-18. The synaptonemal complex is a zipper-like structure that assembles between homologous chromosomes during meiosis to promote recombination. By using sensitive homology detection protocols, we identify divergent orthologues of KKT16-18 in most eukaryotic supergroups, including experimentally established chromosomal axis components, such as Red1 and Rec10 in budding and fission yeast, ASY3-4 in plants and SYCP2-3 in vertebrates. Furthermore, we found 12 recurrent duplications within this ancient eukaryotic SYCP2–3 gene family, providing opportunities for new functional complexes to arise, including KKT16-18 in the kinetoplastid parasite Trypanosoma brucei. We propose the kinetoplastid kinetochore system evolved by repurposing meiotic components of the chromosome synapsis and homologous recombination machinery that were already present in early eukaryotes.
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Affiliation(s)
- Eelco C Tromer
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Groningen, The Netherlands
| | - Thomas A Wemyss
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Patryk Ludzia
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
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9
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Kostygov AY, Karnkowska A, Votýpka J, Tashyreva D, Maciszewski K, Yurchenko V, Lukeš J. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol 2021; 11:200407. [PMID: 33715388 PMCID: PMC8061765 DOI: 10.1098/rsob.200407] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Euglenozoa is a species-rich group of protists, which have extremely diverse lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids, mostly free-living diplonemids, heterotrophic and photosynthetic euglenids, as well as deep-sea symbiontids. Although they form a well-supported monophyletic group, these morphologically rather distinct groups are almost never treated together in a comparative manner, as attempted here. We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is known about viruses infecting euglenozoans, as well as their relationships with ecto- and endosymbiotic bacteria.
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Affiliation(s)
- Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Jan Votýpka
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Daria Tashyreva
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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