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Halliday C, Dean S, Sunter JD, Wheeler RJ. Subcellular protein localisation of Trypanosoma brucei bloodstream form-upregulated proteins maps stage-specific adaptations. Wellcome Open Res 2023; 8:46. [PMID: 37251657 PMCID: PMC10209625 DOI: 10.12688/wellcomeopenres.18586.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
Background: Genome-wide subcellular protein localisation in Trypanosoma brucei, through our TrypTag project, has comprehensively dissected the molecular organisation of this important pathogen. Powerful as this resource is , T. brucei has multiple developmental forms and we previously only analysed the procyclic form. This is an insect life cycle stage, leaving the mammalian bloodstream form unanalysed. The expectation is that between life stages protein localisation would not change dramatically (completely unchanged or shifting to analogous stage-specific structures). However, this has not been specifically tested. Similarly, which organelles tend to contain proteins with stage-specific expression can be predicted from known stage specific adaptations but has not been comprehensively tested. Methods: We used endogenous tagging with mNG to determine the sub-cellular localisation of the majority of proteins encoded by transcripts significantly upregulated in the bloodstream form, and performed comparison to the existing localisation data in procyclic forms. Results: We have confirmed the localisation of known stage-specific proteins and identified the localisation of novel stage-specific proteins. This gave a map of which organelles tend to contain stage specific proteins: the mitochondrion for the procyclic form, and the endoplasmic reticulum, endocytic system and cell surface in the bloodstream form. Conclusions: This represents the first genome-wide map of life cycle stage-specific adaptation of organelle molecular machinery in T. brucei.
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Affiliation(s)
- Clare Halliday
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Samuel Dean
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Jack Daniel Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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Halliday C, Dean S, Sunter JD, Wheeler RJ. Subcellular protein localisation of Trypanosoma brucei bloodstream form-upregulated proteins maps stage-specific adaptations. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18586.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Background: Genome-wide subcellular protein localisation in Trypanosoma brucei, through our TrypTag project, has comprehensively dissected the molecular organisation of this important pathogen. Powerful as this resource is, T. brucei has multiple developmental forms and we previously only analysed the procyclic form. This is an insect life cycle stage, leaving the mammalian bloodstream form unanalysed. The expectation is that between life stages protein localisation would not change dramatically (completely unchanged or shifting to analogous stage-specific structures). However, this has not been specifically tested. Similarly, which organelles tend to contain proteins with stage-specific expression can be predicted from known stage specific adaptations but has not been comprehensively tested. Methods: We used endogenous tagging with mNG to determine the sub-cellular localisation of the majority of proteins encoded by transcripts significantly upregulated in the bloodstream form, and performed comparison to the existing localisation data in procyclic forms. Results: We have confirmed the localisation of known and identified the localisation of novel stage-specific proteins. This gave a map of which organelles tend to contain stage specific proteins: the mitochondrion for the procyclic form, and the endoplasmic reticulum, endocytic system and cell surface in the bloodstream form. Conclusions: This represents the first genome-wide map of life cycle stage-specific adaptation of organelle molecular machinery in T. brucei.
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Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei. Nat Microbiol 2023; 8:533-547. [PMID: 36804636 PMCID: PMC9981465 DOI: 10.1038/s41564-022-01295-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/21/2022] [Indexed: 02/22/2023]
Abstract
Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is challenging because, as with most eukaryotic microbes, ~50% of genome-encoded proteins have completely unknown functions. Here, using fluorescence microscopy and cell lines expressing endogenously tagged proteins, we mapped the subcellular localization of 89% of the T. brucei proteome, a resource we call TrypTag. We provide clues to function and define lineage-specific organelle adaptations for parasitism, mapping the ultraconserved cellular architecture of eukaryotes, including the first comprehensive 'cartographic' analysis of the eukaryotic flagellum, which is vital for morphogenesis and pathology. To demonstrate the power of this resource, we identify novel organelle subdomains and changes in molecular composition through the cell cycle. TrypTag is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.
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Jeilani M, Billington K, Sunter JD, Dean S, Wheeler RJ. Nucleolar targeting in an early-branching eukaryote suggests a general mechanism for ribosome protein sorting. J Cell Sci 2022; 135:jcs259701. [PMID: 36052646 PMCID: PMC9659390 DOI: 10.1242/jcs.259701] [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: 12/18/2021] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
The compartmentalised eukaryotic cell demands accurate targeting of proteins to the organelles in which they function, whether membrane-bound (like the nucleus) or non-membrane-bound (like the nucleolus). Nucleolar targeting relies on positively charged localisation signals and has received rejuvenated interest since the widespread recognition of liquid-liquid phase separation (LLPS) as a mechanism contributing to nucleolus formation. Here, we exploit a new genome-wide analysis of protein localisation in the early-branching eukaryote Trypanosoma brucei to analyse general nucleolar protein properties. T. brucei nucleolar proteins have similar properties to those in common model eukaryotes, specifically basic amino acids. Using protein truncations and addition of candidate targeting sequences to proteins, we show both homopolymer runs and distributed basic amino acids give nucleolar partition, further aided by a nuclear localisation signal (NLS). These findings are consistent with phase separation models of nucleolar formation and physical protein properties being a major contributing mechanism for eukaryotic nucleolar targeting, conserved from the last eukaryotic common ancestor. Importantly, cytoplasmic ribosome proteins, unlike mitochondrial ribosome proteins, have more basic residues - pointing to adaptation of physicochemical properties to assist segregation.
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Affiliation(s)
- Milad Jeilani
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Karen Billington
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Jack Daniel Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Samuel Dean
- Warwick Medical School, Warwick University, Warwick CV4 7AL, UK
| | - Richard John Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK
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Godar S, Oristian J, Hinsch V, Wentworth K, Lopez E, Amlashi P, Enverso G, Markley S, Alper JD. Light chain 2 is a Tctex-type related axonemal dynein light chain that regulates directional ciliary motility in Trypanosoma brucei. PLoS Pathog 2022; 18:e1009984. [PMID: 36155669 PMCID: PMC9536576 DOI: 10.1371/journal.ppat.1009984] [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: 09/27/2021] [Revised: 10/06/2022] [Accepted: 08/26/2022] [Indexed: 01/04/2023] Open
Abstract
Flagellar motility is essential for the cell morphology, viability, and virulence of pathogenic kinetoplastids. Trypanosoma brucei flagella beat with a bending wave that propagates from the flagellum's tip to its base, rather than base-to-tip as in other eukaryotes. Thousands of dynein motor proteins coordinate their activity to drive ciliary bending wave propagation. Dynein-associated light and intermediate chains regulate the biophysical mechanisms of axonemal dynein. Tctex-type outer arm dynein light chain 2 (LC2) regulates flagellar bending wave propagation direction, amplitude, and frequency in Chlamydomonas reinhardtii. However, the role of Tctex-type light chains in regulating T. brucei motility is unknown. Here, we used a combination of bioinformatics, in-situ molecular tagging, and immunofluorescence microscopy to identify a Tctex-type light chain in the procyclic form of T. brucei (TbLC2). We knocked down TbLC2 expression using RNAi in both wild-type and FLAM3, a flagellar attachment zone protein, knockdown cells and quantified TbLC2's effects on trypanosome cell biology and biophysics. We found that TbLC2 knockdown reduced the directional persistence of trypanosome cell swimming, induced an asymmetric ciliary bending waveform, modulated the bias between the base-to-tip and tip-to-base beating modes, and increased the beating frequency. Together, our findings are consistent with a model of TbLC2 as a down-regulator of axonemal dynein activity that stabilizes the forward tip-to-base beating ciliary waveform characteristic of trypanosome cells. Our work sheds light on axonemal dynein regulation mechanisms that contribute to pathogenic kinetoplastids' unique tip-to-base ciliary beating nature and how those mechanisms underlie dynein-driven ciliary motility more generally.
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Affiliation(s)
- Subash Godar
- Department of Physics and Astronomy, College of Science, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - James Oristian
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Valerie Hinsch
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Katherine Wentworth
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Ethan Lopez
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Genetics and Biochemistry, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Parastoo Amlashi
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Gerald Enverso
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Samantha Markley
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
| | - Joshua Daniel Alper
- Department of Physics and Astronomy, College of Science, Clemson University, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
- Department of Biological Sciences, College of Science, Clemson University, Clemson, South Carolina, United States of America
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López-Escobar L, Hänisch B, Halliday C, Ishii M, Akiyoshi B, Dean S, Sunter JD, Wheeler RJ, Gull K. Stage-specific transcription activator ESB1 regulates monoallelic antigen expression in Trypanosoma brucei. Nat Microbiol 2022; 7:1280-1290. [PMID: 35879525 PMCID: PMC9352583 DOI: 10.1038/s41564-022-01175-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
Abstract
Variant surface glycoprotein (VSG) coats bloodstream form Trypanosoma brucei parasites, and monoallelic VSG expression underpins the antigenic variation necessary for pathogenicity. One of thousands of VSG genes is transcribed by RNA polymerase I in a singular nuclear structure called the expression site body (ESB), but how monoallelic VSG transcription is achieved remains unclear. Using a localization screen of 153 proteins we found one, ESB-specific protein 1 (ESB1), that localized only to the ESB and is expressed only in VSG-expressing life cycle stages. ESB1 associates with DNA near the active VSG promoter and is necessary for VSG expression, with overexpression activating inactive VSG promoters. Mechanistically, ESB1 is necessary for recruitment of a subset of ESB components, including RNA polymerase I, revealing that the ESB has separately assembled subdomains. Because many trypanosomatid parasites have divergent ESB1 orthologues yet do not undergo antigenic variation, ESB1 probably represents an important class of transcription regulators.
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Affiliation(s)
| | - Benjamin Hänisch
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Clare Halliday
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Midori Ishii
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Samuel Dean
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Jack Daniel Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
| | | | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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Sáez Conde J, Dean S. Structure, function and druggability of the African trypanosome flagellum. J Cell Physiol 2022; 237:2654-2667. [PMID: 35616248 PMCID: PMC9323424 DOI: 10.1002/jcp.30778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022]
Abstract
African trypanosomes are early branching protists that cause human and animal diseases, termed trypanosomiases. They have been under intensive study for more than 100 years and have contributed significantly to our understanding of eukaryotic biology. The combination of conserved and parasite-specific features mean that their flagellum has gained particular attention. Here, we discuss the different structural features of the flagellum and their role in transmission and virulence. We highlight the possibilities of targeting flagellar function to cure trypanosome infections and help in the fight to eliminate trypanosomiases.
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Affiliation(s)
- Julia Sáez Conde
- Division of Biomedical Sciences, Warwick Medical SchoolUniversity of WarwickCoventryUK
| | - Samuel Dean
- Division of Biomedical Sciences, Warwick Medical SchoolUniversity of WarwickCoventryUK
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