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King SM, Sakato-Antoku M, Patel-King RS, Balsbaugh JL. The methylome of motile cilia. Mol Biol Cell 2024; 35:ar89. [PMID: 38696262 PMCID: PMC11244166 DOI: 10.1091/mbc.e24-03-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/04/2024] Open
Abstract
Cilia are highly complex motile, sensory, and secretory organelles that contain perhaps 1000 or more distinct protein components, many of which are subject to various posttranslational modifications such as phosphorylation, N-terminal acetylation, and proteolytic processing. Another common modification is the addition of one or more methyl groups to the side chains of arginine and lysine residues. These tunable additions delocalize the side-chain charge, decrease hydrogen bond capacity, and increase both bulk and hydrophobicity. Methylation is usually mediated by S-adenosylmethionine (SAM)-dependent methyltransferases and reversed by demethylases. Previous studies have identified several ciliary proteins that are subject to methylation including axonemal dynein heavy chains that are modified by a cytosolic methyltransferase. Here, we have performed an extensive proteomic analysis of multiple independently derived cilia samples to assess the potential for SAM metabolism and the extent of methylation in these organelles. We find that cilia contain all the enzymes needed for generation of the SAM methyl donor and recycling of the S-adenosylhomocysteine and tetrahydrofolate byproducts. In addition, we find that at least 155 distinct ciliary proteins are methylated, in some cases at multiple sites. These data provide a comprehensive resource for studying the consequences of methyl marks on ciliary biology.
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Affiliation(s)
- Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Ramila S. Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 3305
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT 06269
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2
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Field MC. Ras superfamily GTPases and signal transduction in Euglena gracilis. Protist 2024; 175:126017. [PMID: 38295671 DOI: 10.1016/j.protis.2024.126017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/21/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024]
Abstract
Biological complexity is challenging to define, but can be considered through one or more features, including overall genome size, number of genes, morphological features, multicellularity, number of life cycle stages and the ability to adapt to different environments. Euglena gracilis meets several of these criteria, with a large genome of ∼38,000 protein coding genes and a considerable ability to survive under many different conditions, some of which can be described as challenging or harsh. Potential molecular exemplars of complexity tying these aspects together are signalling pathways, including GTPases, kinases and ubiquitylation, which increase the functionality of the gene-encoded proteome manyfold. Each of these examples can modulate both protein activity and gene expression. To address the connection between genome size and complexity I have undertaken a brief, and somewhat qualitative, survey of the small ras-like GTPase superfamily of E. gracilis. Unexpectedly, apart from Rab-GTPases which control intracellular transport and organelle identify, the size of the GTPase cohort is modest, and, for example, has not scaled with gene number when compared to the close relatives, trypanosomatids. I suggest that understanding the functions of this protein family will be vital to uncovering the complexity of E. gracilis biology.
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Affiliation(s)
- Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK; Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
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3
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Bachmaier S, Gould MK, Polatoglou E, Omelianczyk R, Brennand AE, Aloraini MA, Munday JC, Horn D, Boshart M, de Koning HP. Novel kinetoplastid-specific cAMP binding proteins identified by RNAi screening for cAMP resistance in Trypanosoma brucei. Front Cell Infect Microbiol 2023; 13:1204707. [PMID: 37475965 PMCID: PMC10354285 DOI: 10.3389/fcimb.2023.1204707] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/14/2023] [Indexed: 07/22/2023] Open
Abstract
Cyclic AMP signalling in trypanosomes differs from most eukaryotes due to absence of known cAMP effectors and cAMP independence of PKA. We have previously identified four genes from a genome-wide RNAi screen for resistance to the cAMP phosphodiesterase (PDE) inhibitor NPD-001. The genes were named cAMP Response Protein (CARP) 1 through 4. Here, we report an additional six CARP candidate genes from the original sample, after deep sequencing of the RNA interference target pool retrieved after NPD-001 selection (RIT-seq). The resistance phenotypes were confirmed by individual RNAi knockdown. Highest level of resistance to NPD-001, approximately 17-fold, was seen for knockdown of CARP7 (Tb927.7.4510). CARP1 and CARP11 contain predicted cyclic AMP binding domains and bind cAMP as evidenced by capture and competition on immobilised cAMP. CARP orthologues are strongly enriched in kinetoplastid species, and CARP3 and CARP11 are unique to Trypanosoma. Localization data and/or domain architecture of all CARPs predict association with the T. brucei flagellum. This suggests a crucial role of cAMP in flagellar function, in line with the cell division phenotype caused by high cAMP and the known role of the flagellum for cytokinesis. The CARP collection is a resource for discovery of unusual cAMP pathways and flagellar biology.
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Affiliation(s)
- Sabine Bachmaier
- Faculty of Biology, Genetics, Ludwig-Maximillians University Munich (LMU), Martinsried, Germany
| | - Matthew K. Gould
- Faculty of Biology, Genetics, Ludwig-Maximillians University Munich (LMU), Martinsried, Germany
| | - Eleni Polatoglou
- Faculty of Biology, Genetics, Ludwig-Maximillians University Munich (LMU), Martinsried, Germany
| | - Radoslaw Omelianczyk
- Faculty of Biology, Genetics, Ludwig-Maximillians University Munich (LMU), Martinsried, Germany
| | - Ana E. Brennand
- Faculty of Biology, Genetics, Ludwig-Maximillians University Munich (LMU), Martinsried, Germany
| | - Maha A. Aloraini
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jane C. Munday
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David Horn
- The Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael Boshart
- Faculty of Biology, Genetics, Ludwig-Maximillians University Munich (LMU), Martinsried, Germany
| | - Harry P. de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria). mBio 2023; 14:e0030223. [PMID: 36939357 PMCID: PMC10127745 DOI: 10.1128/mbio.00302-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria-the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1, -3, -4, -4L, -5, and -7, cob, cox1, -2, and -3, and atp1, -6, and -9, with forams and radiolarians additionally carrying nad2 and nad6, respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.
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Ishikawa M, Nomura T, Tamaki S, Ozasa K, Suzuki T, Toyooka K, Hirota K, Yamada K, Suzuki K, Mochida K. CRISPR/Cas9-mediated generation of non-motile mutants to improve the harvesting efficiency of mass-cultivated Euglena gracilis. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2042-2044. [PMID: 35916139 PMCID: PMC9616515 DOI: 10.1111/pbi.13904] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Marumi Ishikawa
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for ScienceTechnology and Innovation HubYokohamaJapan
| | - Toshihisa Nomura
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for ScienceTechnology and Innovation HubYokohamaJapan
- Bioproductivity Informatics Research TeamRIKEN Center for Sustainable Resource ScienceYokohamaJapan
| | - Shun Tamaki
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for ScienceTechnology and Innovation HubYokohamaJapan
| | - Kazunari Ozasa
- Advanced Laser Processing Research TeamRIKEN Center for Advanced PhotonicsWakoJapan
| | - Tomoko Suzuki
- Mass Spectrometry and Microscopy Unit, Technology Platform DivisionRIKEN Center for Sustainable Resource ScienceKanagawaJapan
- Center for Gene ResearchNagoya UniversityAichiJapan
| | - Kiminori Toyooka
- Mass Spectrometry and Microscopy Unit, Technology Platform DivisionRIKEN Center for Sustainable Resource ScienceKanagawaJapan
| | - Kikue Hirota
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for ScienceTechnology and Innovation HubYokohamaJapan
| | - Koji Yamada
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for ScienceTechnology and Innovation HubYokohamaJapan
- euglena Co., Ltd.TokyoJapan
| | - Kengo Suzuki
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for ScienceTechnology and Innovation HubYokohamaJapan
- euglena Co., Ltd.TokyoJapan
| | - Keiichi Mochida
- Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for ScienceTechnology and Innovation HubYokohamaJapan
- Bioproductivity Informatics Research TeamRIKEN Center for Sustainable Resource ScienceYokohamaJapan
- Kihara Institute for Biological ResearchYokohama City UniversityYokohamaJapan
- Graduate School of NanobioscienceYokohama City UniversityYokohamaJapan
- School of Information and Data SciencesNagasaki UniversityNagasakiJapan
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Zoltner M, Field MC. Microbe Profile: Euglena gracilis: photogenic, flexible and hardy. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36178464 DOI: 10.1099/mic.0.001241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Euglena gracilis is a unicellular photosynthetic eukaryotic flagellate of the Discoba supergroup, which also encompasses Kinetoplastida and Diplonema. Plastids have green algal origin and are secondarily acquired. The nuclear genome is extremely large and many genes suggest multiple endosymbiotic/gene transfer events, i.e. derivation from prokaryotes of various lineages. E. gracilis is remarkably robust and can proliferate in environments contaminated with heavy metals and acids. Extraordinary metabolic plasticity and a mixotrophic lifestyle confers an ability to thrive in a broad range of environments, as well as facilitating production of many novel metabolites, making Euglena of considerable biotechnological importance.
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Affiliation(s)
- Martin Zoltner
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czechia
| | - Mark C Field
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czechia.,School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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Kaszecki E, Kennedy V, Shah M, Maciszewski K, Karnkowska A, Linton E, Ginger ML, Farrow S, Ebenezer TE. Meeting Report: Euglenids in the Age of Symbiogenesis: Origins, Innovations, and Prospects, November 8-11, 2021. Protist 2022; 173:125894. [PMID: 35772300 DOI: 10.1016/j.protis.2022.125894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 10/18/2022]
Affiliation(s)
- Emma Kaszecki
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Victoria Kennedy
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Mahfuzur Shah
- Department of Cell Biology, Metabolism and Systems Biology, Noblegen Inc., 2140 East Bank Dr, Peterborough, ON, Canada
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Eric Linton
- Central Michigan University, Department of Biology, Mount Pleasant, MI 48859, USA
| | - Michael L Ginger
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Scott Farrow
- Department of Cell Biology, Metabolism and Systems Biology, Noblegen Inc., 2140 East Bank Dr, Peterborough, ON, Canada
| | - ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
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Molecular Cross-Talk between Gravity- and Light-Sensing Mechanisms in Euglena gracilis. Int J Mol Sci 2022; 23:ijms23052776. [PMID: 35269918 PMCID: PMC8911436 DOI: 10.3390/ijms23052776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/19/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
Euglena gracilis is a photosynthetic flagellate. To acquire a suitable position in its surrounding aquatic environment, it exploits light and gravity primarily as environmental cues. Several physiological studies have indicated a fine-tuned relationship between gravity sensing (gravitaxis) and light sensing in E. gracilis. However, the underlying molecular mechanism is largely unknown. The photoreceptor photoactivated adenylyl cyclase (PAC) has been studied for over a decade. Nevertheless, no direct/indirect interaction partner (upstream/downstream) has been reported for PAC. It has been shown that a specific protein, kinase A (PKA), showed to be involved in phototaxis and gravitaxis. The current study reports the localization of the specific PKA and its relationship with PAC.
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