1
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Cayla M, Spanos C, McWilliam K, Waskett E, Rappsilber J, Matthews KR. Differentiation granules, a dynamic regulator of T. brucei development. Nat Commun 2024; 15:2972. [PMID: 38582942 PMCID: PMC10998879 DOI: 10.1038/s41467-024-47309-1] [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: 10/13/2023] [Accepted: 03/26/2024] [Indexed: 04/08/2024] Open
Abstract
Adaptation to a change of environment is an essential process for survival, in particular for parasitic organisms exposed to a wide range of hosts. Such adaptations include rapid control of gene expression through the formation of membraneless organelles composed of poly-A RNA and proteins. The African trypanosome Trypanosoma brucei is exquisitely sensitive to well-defined environmental stimuli that trigger cellular adaptations through differentiation events that characterise its complex life cycle. The parasite has been shown to form stress granules in vitro, and it has been proposed that such a stress response could have been repurposed to enable differentiation and facilitate parasite transmission. Therefore, we explored the composition and positional dynamics of membraneless granules formed in response to starvation stress and during differentiation in the mammalian host between the replicative slender and transmission-adapted stumpy forms. We find that T. brucei differentiation does not reflect the default response to environmental stress. Instead, the developmental response of the parasites involves a specific and programmed hierarchy of membraneless granule assembly, with distinct components and regulation by protein kinases such as TbDYRK, that are required for the parasite to successfully progress through its life cycle development and prepare for transmission.
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Affiliation(s)
- Mathieu Cayla
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
- York Biomedical Research Institute, Department of Biology, University of York, York, UK.
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kirsty McWilliam
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Eliza Waskett
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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2
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Morrison LJ, Steketee PC, Tettey MD, Matthews KR. Pathogenicity and virulence of African trypanosomes: From laboratory models to clinically relevant hosts. Virulence 2023; 14:2150445. [PMID: 36419235 DOI: 10.1080/21505594.2022.2150445] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
African trypanosomes are vector-borne protozoa, which cause significant human and animal disease across sub-Saharan Africa, and animal disease across Asia and South America. In humans, infection is caused by variants of Trypanosoma brucei, and is characterized by varying rate of progression to neurological disease, caused by parasites exiting the vasculature and entering the brain. Animal disease is caused by multiple species of trypanosome, primarily T. congolense, T. vivax, and T. brucei. These trypanosomes also infect multiple species of mammalian host, and this complexity of trypanosome and host diversity is reflected in the spectrum of severity of disease in animal trypanosomiasis, ranging from hyperacute infections associated with mortality to long-term chronic infections, and is also a main reason why designing interventions for animal trypanosomiasis is so challenging. In this review, we will provide an overview of the current understanding of trypanosome determinants of infection progression and severity, covering laboratory models of disease, as well as human and livestock disease. We will also highlight gaps in knowledge and capabilities, which represent opportunities to both further our fundamental understanding of how trypanosomes cause disease, as well as facilitating the development of the novel interventions that are so badly needed to reduce the burden of disease caused by these important pathogens.
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Affiliation(s)
- Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Pieter C Steketee
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Mabel D Tettey
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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3
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McWilliam KR. Cell-cell communication in African trypanosomes. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001388. [PMID: 37643128 PMCID: PMC10482365 DOI: 10.1099/mic.0.001388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Years of research have shown us that unicellular organisms do not exist entirely in isolation, but rather that they are capable of an altogether far more sociable way of living. Single cells produce, receive and interpret signals, coordinating and changing their behaviour according to the information received. Although this cell-cell communication has long been considered the norm in the bacterial world, an increasing body of knowledge is demonstrating that single-celled eukaryotic parasites also maintain active social lives. This communication can drive parasite development, facilitate the invasion of new niches and, ultimately, influence infection outcome. In this review, I present the evidence for cell-cell communication during the life cycle of the African trypanosomes, from their mammalian hosts to their insect vectors, and reflect on the many remaining unanswered questions in this fascinating field.
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Affiliation(s)
- K. R. McWilliam
- Institute for Immunology and Infection Research, School of Biological Sciences, King’s Buildings, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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4
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Marcelino TDP, Fala AM, da Silva MM, Souza-Melo N, Malvezzi AM, Klippel AH, Zoltner M, Padilla-Mejia N, Kosto S, Field MC, Burle-Caldas GDA, Teixeira SMR, Couñago RM, Massirer KB, Schenkman S. Identification of inhibitors for the transmembrane Trypanosoma cruzi eIF2α kinase relevant for parasite proliferation. J Biol Chem 2023; 299:104857. [PMID: 37230387 PMCID: PMC10300260 DOI: 10.1016/j.jbc.2023.104857] [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: 03/05/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
The TcK2 protein kinase of Trypanosoma cruzi, the causative agent of Chagas disease, is structurally similar to the human kinase PERK, which phosphorylates the initiation factor eIF2α and, in turn, inhibits translation initiation. We have previously shown that absence of TcK2 kinase impairs parasite proliferation within mammalian cells, positioning it as a potential target for treatment of Chagas disease. To better understand its role in the parasite, here we initially confirmed the importance of TcK2 in parasite proliferation by generating CRISPR/Cas9 TcK2-null cells, albeit they more efficiently differentiate into infective forms. Proteomics indicates that the TcK2 knockout of proliferative forms expresses proteins including trans-sialidases, normally restricted to infective and nonproliferative trypomastigotes explaining decreased proliferation and better differentiation. TcK2 knockout cells lost phosphorylation of eukaryotic initiation factor 3 and cyclic AMP responsive-like element, recognized to promote growth, likely explaining both decreased proliferation and augmented differentiation. To identify specific inhibitors, a library of 379 kinase inhibitors was screened by differential scanning fluorimetry using a recombinant TcK2 encompassing the kinase domain and selected molecules were tested for kinase inhibition. Only Dasatinib and PF-477736, inhibitors of Src/Abl and ChK1 kinases, showed inhibitory activity with IC50 of 0.2 ± 0.02 mM and 0.8 ± 0.1, respectively. In infected cells Dasatinib inhibited growth of parental amastigotes (IC50 = 0.6 ± 0.2 mM) but not TcK2 of depleted parasites (IC50 > 34 mM) identifying Dasatinib as a potential lead for development of therapeutics for Chagas disease targeting TcK2.
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Affiliation(s)
- Tiago de Paula Marcelino
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Angela Maria Fala
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Matheus Monteiro da Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Normanda Souza-Melo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Amaranta Muniz Malvezzi
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Angélica Hollunder Klippel
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil; Departamento de Ciências Biológicas da Faculdade de Ciências Farmacêuticas da Universidade Estadual Paulista "Júlio de Mesquita Filho"-Unesp, Araraquara, SP, Brazil
| | - Martin Zoltner
- Drug Discovery and Evaluation Unit, Department of Parasitology, Faculty of Science, Charles University in Prague, BIOCEV, Vestec, Czech Republic
| | | | - Samantha Kosto
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK; Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | | | - Rafael Miguez Couñago
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering - CBMEG, Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, Campinas, SP, Brazil.
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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Briggs EM, Marques CA, Oldrieve GR, Hu J, Otto TD, Matthews KR. Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single-cell transcriptomics. eLife 2023; 12:e86325. [PMID: 37166108 PMCID: PMC10212563 DOI: 10.7554/elife.86325] [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: 01/20/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023] Open
Abstract
African trypanosomes proliferate as bloodstream forms (BSFs) and procyclic forms in the mammal and tsetse fly midgut, respectively. This allows them to colonise the host environment upon infection and ensure life cycle progression. Yet, understanding of the mechanisms that regulate and drive the cell replication cycle of these forms is limited. Using single-cell transcriptomics on unsynchronised cell populations, we have obtained high resolution cell cycle regulated (CCR) transcriptomes of both procyclic and slender BSF Trypanosoma brucei without prior cell sorting or synchronisation. Additionally, we describe an efficient freeze-thawing protocol that allows single-cell transcriptomic analysis of cryopreserved T. brucei. Computational reconstruction of the cell cycle using periodic pseudotime inference allowed the dynamic expression patterns of cycling genes to be profiled for both life cycle forms. Comparative analyses identify a core cycling transcriptome highly conserved between forms, as well as several genes where transcript levels dynamics are form specific. Comparing transcript expression patterns with protein abundance revealed that the majority of genes with periodic cycling transcript and protein levels exhibit a relative delay between peak transcript and protein expression. This work reveals novel detail of the CCR transcriptomes of both forms, which are available for further interrogation via an interactive webtool.
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Affiliation(s)
- Emma M Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Catarina A Marques
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Guy R Oldrieve
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Jihua Hu
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Thomas D Otto
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
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6
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Poudyal NR, Paul KS. Fatty acid uptake in Trypanosoma brucei: Host resources and possible mechanisms. Front Cell Infect Microbiol 2022; 12:949409. [PMID: 36478671 PMCID: PMC9719944 DOI: 10.3389/fcimb.2022.949409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022] Open
Abstract
Trypanosoma brucei spp. causes African Sleeping Sickness in humans and nagana, a wasting disease, in cattle. As T. brucei goes through its life cycle in its mammalian and insect vector hosts, it is exposed to distinct environments that differ in their nutrient resources. One such nutrient resource is fatty acids, which T. brucei uses to build complex lipids or as a potential carbon source for oxidative metabolism. Of note, fatty acids are the membrane anchoring moiety of the glycosylphosphatidylinositol (GPI)-anchors of the major surface proteins, Variant Surface Glycoprotein (VSG) and the Procyclins, which are implicated in parasite survival in the host. While T. brucei can synthesize fatty acids de novo, it also readily acquires fatty acids from its surroundings. The relative contribution of parasite-derived vs. host-derived fatty acids to T. brucei growth and survival is not known, nor have the molecular mechanisms of fatty acid uptake been defined. To facilitate experimental inquiry into these important aspects of T. brucei biology, we addressed two questions in this review: (1) What is known about the availability of fatty acids in different host tissues where T. brucei can live? (2) What is known about the molecular mechanisms mediating fatty acid uptake in T. brucei? Finally, based on existing biochemical and genomic data, we suggest a model for T. brucei fatty acid uptake that proposes two major routes of fatty acid uptake: diffusion across membranes followed by intracellular trapping, and endocytosis of host lipoproteins.
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Affiliation(s)
- Nava Raj Poudyal
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States,Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States
| | - Kimberly S. Paul
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States,Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States,*Correspondence: Kimberly S. Paul,
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7
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Cayla M, Nievas YR, Matthews KR, Mottram JC. Distinguishing functions of trypanosomatid protein kinases. Trends Parasitol 2022; 38:950-961. [PMID: 36075845 DOI: 10.1016/j.pt.2022.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 01/13/2023]
Abstract
Trypanosomatid parasitic protozoa are divergent from opisthokont models and have evolved unique mechanisms to regulate their complex life cycles and to adapt to a range of hosts. Understanding how these organisms respond, adapt, and persist in their different hosts could reveal optimal drug-control strategies. Protein kinases are fundamental to many biological processes such as cell cycle control, adaptation to stress, and cellular differentiation. Therefore, we have focused this review on the features and functions of protein kinases that distinguish trypanosomatid kinomes from other eukaryotes. We describe the latest research, highlighting similarities and differences between two groups of trypanosomatid parasites, Leishmania and African trypanosomes.
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Affiliation(s)
- Mathieu Cayla
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Y Romina Nievas
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK.
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Genomic Occupancy of the Bromodomain Protein Bdf3 Is Dynamic during Differentiation of African Trypanosomes from Bloodstream to Procyclic Forms. mSphere 2022; 7:e0002322. [PMID: 35642518 PMCID: PMC9241505 DOI: 10.1128/msphere.00023-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Trypanosoma brucei, the causative agent of human and animal African trypanosomiasis, cycles between a mammalian host and a tsetse fly vector. The parasite undergoes huge changes in morphology and metabolism during adaptation to each host environment. These changes are reflected in the different transcriptomes of parasites living in each host. However, it remains unclear whether chromatin-interacting proteins help mediate these changes. Bromodomain proteins localize to transcription start sites in bloodstream parasites, but whether the localization of bromodomain proteins changes as parasites differentiate from bloodstream to insect stages remains unknown. To address this question, we performed cleavage under target and release using nuclease (CUT&RUN) against bromodomain protein 3 (Bdf3) in parasites differentiating from bloodstream to insect forms. We found that Bdf3 occupancy at most loci increased at 3 h following onset of differentiation and decreased thereafter. A number of sites with increased bromodomain protein occupancy lie proximal to genes with altered transcript levels during differentiation, such as procyclins, procyclin-associated genes, and invariant surface glycoproteins. Most Bdf3-occupied sites are observed throughout differentiation. However, one site appears de novo during differentiation and lies proximal to the procyclin gene locus housing genes essential for remodeling surface proteins following transition to the insect stage. These studies indicate that occupancy of chromatin-interacting proteins is dynamic during life cycle stage transitions and provide the groundwork for future studies on the effects of changes in bromodomain protein occupancy. Additionally, the adaptation of CUT&RUN for Trypanosoma brucei provides other researchers with an alternative to chromatin immunoprecipitation (ChIP). IMPORTANCE The parasite Trypanosoma brucei is the causative agent of human and animal African trypanosomiasis (sleeping sickness). Trypanosomiasis, which affects humans and cattle, is fatal if untreated. Existing drugs have significant side effects. Thus, these parasites impose a significant human and economic burden in sub-Saharan Africa, where trypanosomiasis is endemic. T. brucei cycles between the mammalian host and a tsetse fly vector, and parasites undergo huge changes in morphology and metabolism to adapt to different hosts. Here, we show that DNA-interacting bromodomain protein 3 (Bdf3) shows changes in occupancy at its binding sites as parasites transition from the bloodstream to the insect stage. Additionally, a new binding site appears near the locus responsible for remodeling of parasite surface proteins during transition to the insect stage. Understanding the mechanisms behind host adaptation is important for understanding the life cycle of the parasite.
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9
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Oldrieve GR, Malacart B, López-Vidal J, Matthews KR. The genomic basis of host and vector specificity in non-pathogenic trypanosomatids. Biol Open 2022; 11:bio059237. [PMID: 35373253 PMCID: PMC9099014 DOI: 10.1242/bio.059237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/25/2022] [Indexed: 11/20/2022] Open
Abstract
Trypanosoma theileri, a non-pathogenic parasite of bovines, has a predicted surface protein architecture that likely aids survival in its mammalian host. Their surface proteins are encoded by genes which account for ∼10% of their genome. A non-pathogenic parasite of sheep, Trypanosoma melophagium, is transmitted by the sheep ked and is closely related to T. theileri. To explore host and vector specificity between these species, we sequenced the T. melophagium genome and transcriptome and an annotated draft genome was assembled. T. melophagium was compared to 43 kinetoplastid genomes, including T. theileri. T. melophagium and T. theileri have an AT biased genome, the greatest bias of publicly available trypanosomatids. This trend may result from selection acting to decrease the genomic nucleotide cost. The T. melophagium genome is 6.3Mb smaller than T. theileri and large families of proteins, characteristic of the predicted surface of T. theileri, were found to be absent or greatly reduced in T. melophagium. Instead, T. melophagium has modestly expanded protein families associated with the avoidance of complement-mediated lysis. We propose that the contrasting genomic features of these species is linked to their mode of transmission from their insect vector to their mammalian host. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Guy R. Oldrieve
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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10
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Trypanosoma brucei Tim50 Possesses PAP Activity and Plays a Critical Role in Cell Cycle Regulation and Parasite Infectivity. mBio 2021; 12:e0159221. [PMID: 34517757 PMCID: PMC8546626 DOI: 10.1128/mbio.01592-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Trypanosoma brucei, the infective agent for African trypanosomiasis, possesses a homologue of the translocase of the mitochondrial inner membrane 50 (TbTim50). It has a pair of characteristic phosphatase signature motifs, DXDX(T/V). Here, we demonstrated that, besides its protein phosphatase activity, the recombinant TbTim50 binds and hydrolyzes phosphatidic acid in a concentration-dependent manner. Mutations of D242 and D244, but not of D345and D347, to alanine abolished these activities. In silico structural homology models identified the putative binding interfaces that may accommodate different phosphosubstrates. Interestingly, TbTim50 depletion in the bloodstream form (BF) of T. brucei reduced cardiolipin (CL) levels and decreased mitochondrial membrane potential (ΔΨ). TbTim50 knockdown (KD) also reduced the population of G2/M phase and increased that of G1 phase cells; inhibited segregation and caused overreplication of kinetoplast DNA (kDNA), and reduced BF cell growth. Depletion of TbTim50 increased the levels of AMPK phosphorylation, and parasite morphology was changed with upregulation of expression of a few stumpy marker genes. Importantly, we observed that TbTim50-depleted parasites were unable to establish infection in mice. Proteomics analysis showed reductions in levels of the translation factors, flagellar transport proteins, and many proteasomal subunits, including those of the mitochondrial heat shock locus ATPase (HslVU), which is known to play a role in regulation of kinetoplast DNA (kDNA) replication. Reduction of the level of HslV in TbTim50 KD cells was further validated by immunoblot analysis. Together, our results showed that TbTim50 is essential for mitochondrial function, regulation of kDNA replication, and the cell cycle in the BF. Therefore, TbTim50 is an important target for structure-based drug design to combat African trypanosomiasis.
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11
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Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing. Nat Commun 2021; 12:5268. [PMID: 34489460 PMCID: PMC8421343 DOI: 10.1038/s41467-021-25607-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Developmental steps in the trypanosome life-cycle involve transition between replicative and non-replicative forms specialised for survival in, and transmission between, mammalian and tsetse fly hosts. Here, using oligopeptide-induced differentiation in vitro, we model the progressive development of replicative 'slender' to transmissible 'stumpy' bloodstream form Trypanosoma brucei and capture the transcriptomes of 8,599 parasites using single cell transcriptomics (scRNA-seq). Using this framework, we detail the relative order of biological events during asynchronous development, profile dynamic gene expression patterns and identify putative regulators. We additionally map the cell cycle of proliferating parasites and position stumpy cell-cycle exit at early G1 before progression to a distinct G0 state. A null mutant for one transiently elevated developmental regulator, ZC3H20 is further analysed by scRNA-seq, identifying its point of failure in the developmental atlas. This approach provides a paradigm for the dissection of differentiation events in parasites, relevant to diverse transitions in pathogen biology.
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12
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Abstract
African trypanosomes are responsible for important diseases of humans and animals in sub-Saharan Africa. The best-studied species is Trypanosoma brucei, which is characterized by development in the mammalian host between morphologically slender and stumpy forms. The latter are adapted for transmission by the parasite's vector, the tsetse fly. The development of stumpy forms is driven by density-dependent quorum-sensing (QS), the molecular basis for which is now coming to light. In this review, I discuss the historical context and biological features of trypanosome QS and how it contributes to the parasite's infection dynamics within its mammalian host. Also, I discuss how QS can be lost in different trypanosome species, such as T. brucei evansi and T. brucei equiperdum, or modulated when parasites find themselves competing with others of different genotypes or of different trypanosome species in the same host. Finally, I consider the potential to exploit trypanosome QS therapeutically. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Keith R Matthews
- Institute for Immunology and Infection Research, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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13
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Luzak V, López-Escobar L, Siegel TN, Figueiredo LM. Cell-to-Cell Heterogeneity in Trypanosomes. Annu Rev Microbiol 2021; 75:107-128. [PMID: 34228491 DOI: 10.1146/annurev-micro-040821-012953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent developments in single-cell and single-molecule techniques have revealed surprising levels of heterogeneity among isogenic cells. These advances have transformed the study of cell-to-cell heterogeneity into a major area of biomedical research, revealing that it can confer essential advantages, such as priming populations of unicellular organisms for future environmental stresses. Protozoan parasites, such as trypanosomes, face multiple and often hostile environments, and to survive, they undergo multiple changes, including changes in morphology, gene expression, and metabolism. But why does only a subset of proliferative cells differentiate to the next life cycle stage? Why do only some bloodstream parasites undergo antigenic switching while others stably express one variant surface glycoprotein? And why do some parasites invade an organ while others remain in the bloodstream? Building on extensive research performed in bacteria, here we suggest that biological noise can contribute to the fitness of eukaryotic pathogens and discuss the importance of cell-to-cell heterogeneity in trypanosome infections. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Vanessa Luzak
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany.,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany
| | - Lara López-Escobar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal;
| | - T Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany.,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich 82152, Germany
| | - Luisa M Figueiredo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal;
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Walsh B, Hill KL. Right place, right time: Environmental sensing and signal transduction directs cellular differentiation and motility in Trypanosoma brucei. Mol Microbiol 2021; 115:930-941. [PMID: 33434370 DOI: 10.1111/mmi.14682] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 11/29/2022]
Abstract
Trypanosoma brucei and other African trypanosomes are vector-borne parasites that cause substantial human suffering across sub-Saharan Africa. The T. brucei life cycle is punctuated by numerous developmental stages, each occurring in a specific environmental niche and characterized by a unique morphology, metabolism, surface protein coat, and gene expression profile. The environmental cues and signaling pathways that drive transitions between these stages remain incompletely understood. Recent studies have started to fill this gap in knowledge. Likewise, several new studies have expanded our understanding of parasite movement through specific tissues and the parasite's ability to alter movement in response to external cues. Life cycle stage differentiation and motility are intimately integrated phenomena, as parasites must be at the right place (i.e., within a specific environmental milieu) at the right time (i.e., when they are appropriately staged and preadapted for perceiving and responding to signals) in order to complete their life cycle. In this review, we highlight some of the recent work that has transformed our understanding of signaling events that control parasite differentiation and motility. Increased knowledge of T. brucei environmental sensing and signal transduction advances our understanding of parasite biology and may direct prospective chemotherapeutic and transmission blockade strategies that are critical to eradication efforts.
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Affiliation(s)
- Breanna Walsh
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.,Medical Scientist Training Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Kent L Hill
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA.,California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
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15
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Lindberg MF, Meijer L. Dual-Specificity, Tyrosine Phosphorylation-Regulated Kinases (DYRKs) and cdc2-Like Kinases (CLKs) in Human Disease, an Overview. Int J Mol Sci 2021; 22:6047. [PMID: 34205123 PMCID: PMC8199962 DOI: 10.3390/ijms22116047] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/09/2023] Open
Abstract
Dual-specificity tyrosine phosphorylation-regulated kinases (DYRK1A, 1B, 2-4) and cdc2-like kinases (CLK1-4) belong to the CMGC group of serine/threonine kinases. These protein kinases are involved in multiple cellular functions, including intracellular signaling, mRNA splicing, chromatin transcription, DNA damage repair, cell survival, cell cycle control, differentiation, homocysteine/methionine/folate regulation, body temperature regulation, endocytosis, neuronal development, synaptic plasticity, etc. Abnormal expression and/or activity of some of these kinases, DYRK1A in particular, is seen in many human nervous system diseases, such as cognitive deficits associated with Down syndrome, Alzheimer's disease and related diseases, tauopathies, dementia, Pick's disease, Parkinson's disease and other neurodegenerative diseases, Phelan-McDermid syndrome, autism, and CDKL5 deficiency disorder. DYRKs and CLKs are also involved in diabetes, abnormal folate/methionine metabolism, osteoarthritis, several solid cancers (glioblastoma, breast, and pancreatic cancers) and leukemias (acute lymphoblastic leukemia, acute megakaryoblastic leukemia), viral infections (influenza, HIV-1, HCMV, HCV, CMV, HPV), as well as infections caused by unicellular parasites (Leishmania, Trypanosoma, Plasmodium). This variety of pathological implications calls for (1) a better understanding of the regulations and substrates of DYRKs and CLKs and (2) the development of potent and selective inhibitors of these kinases and their evaluation as therapeutic drugs. This article briefly reviews the current knowledge about DYRK/CLK kinases and their implications in human disease.
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Affiliation(s)
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France;
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16
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Quintana JF, Zoltner M, Field MC. Evolving Differentiation in African Trypanosomes. Trends Parasitol 2021; 37:296-303. [PMID: 33309505 DOI: 10.1016/j.pt.2020.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Differentiation is a central aspect of the parasite life cycle and encompasses adaptation to both host and environment. If we accept that evolution cannot anticipate an organism's needs as it enters a new environment, how do parasite differentiation pathways arise? The transition between vertebrate and insect stage African trypanosomes is probably one of the better studied and involves a cell-cycle arrested or 'stumpy' form that activates metabolic pathways advantageous to the parasite in the insect host. However, a range of stimuli and stress conditions can trigger similar changes, leading to formation of stumpy-like cellular states. We propose that the origin and optimisation of this differentiation program represents repurposing of a generic stress response to gain considerable gain-of-fitness associated with parasite transmission.
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Affiliation(s)
- Juan F Quintana
- Wellcome Centre for Integrative Parasitology, College of Medical, Veterinary and Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, UK; School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic.
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17
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Rojas F, Cayla M, Matthews KR. Basement membrane proteins as a substrate for efficient Trypanosoma brucei differentiation in vitro. PLoS Negl Trop Dis 2021; 15:e0009284. [PMID: 33909626 PMCID: PMC8109799 DOI: 10.1371/journal.pntd.0009284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/10/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
The ability to reproduce the developmental events of trypanosomes that occur in their mammalian host in vitro offers significant potential to assist in understanding of the underlying biology of the process. For example, the transition from bloodstream slender to bloodstream stumpy forms is a quorum-sensing response to the parasite-derived peptidase digestion products of environmental proteins. As an abundant physiological substrate in vivo, we studied the ability of a basement membrane matrix enriched gel (BME) in the culture medium to support differentiation of pleomorphic Trypanosoma brucei to stumpy forms. BME comprises extracellular matrix proteins, which are among the most abundant proteins found in connective tissues in mammals and known substrates of parasite-released peptidases. We previously showed that two of these released peptidases are involved in generating a signal that promotes slender-to-stumpy differentiation. Here, we tested the ability of basement membrane extract to enhance parasite differentiation through its provision of suitable substrates to generate the quorum sensing signal, namely oligopeptides. Our results show that when grown in the presence of BME, T. brucei pleomorphic cells arrest at the G0/1 phase of the cell cycle and express the differentiation marker PAD1, the response being restricted to differentiation-competent parasites. Further, the stumpy forms generated in BME medium are able to efficiently proceed onto the next life cycle stage in vitro, procyclic forms, when incubated with cis-aconitate, further validating the in vitro BME differentiation system. Hence, BME provides a suitable in vitro substrate able to accurately recapitulate physiological parasite differentiation without the use of experimental animals.
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Affiliation(s)
- Federico Rojas
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mathieu Cayla
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Keith R. Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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18
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Baker N, Catta-Preta CMC, Neish R, Sadlova J, Powell B, Alves-Ferreira EVC, Geoghegan V, Carnielli JBT, Newling K, Hughes C, Vojtkova B, Anand J, Mihut A, Walrad PB, Wilson LG, Pitchford JW, Volf P, Mottram JC. Systematic functional analysis of Leishmania protein kinases identifies regulators of differentiation or survival. Nat Commun 2021; 12:1244. [PMID: 33623024 PMCID: PMC7902614 DOI: 10.1038/s41467-021-21360-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/13/2021] [Indexed: 01/31/2023] Open
Abstract
Differentiation between distinct stages is fundamental for the life cycle of intracellular protozoan parasites and for transmission between hosts, requiring stringent spatial and temporal regulation. Here, we apply kinome-wide gene deletion and gene tagging in Leishmania mexicana promastigotes to define protein kinases with life cycle transition roles. Whilst 162 are dispensable, 44 protein kinase genes are refractory to deletion in promastigotes and are likely core genes required for parasite replication. Phenotyping of pooled gene deletion mutants using bar-seq and projection pursuit clustering reveal functional phenotypic groups of protein kinases involved in differentiation from metacyclic promastigote to amastigote, growth and survival in macrophages and mice, colonisation of the sand fly and motility. This unbiased interrogation of protein kinase function in Leishmania allows targeted investigation of organelle-associated signalling pathways required for successful intracellular parasitism.
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Affiliation(s)
- N Baker
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - C M C Catta-Preta
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - R Neish
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - J Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - B Powell
- Department of Mathematics, University of York, York, UK
| | - E V C Alves-Ferreira
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - V Geoghegan
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - J B T Carnielli
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - K Newling
- Department of Biology, University of York, York, UK
| | - C Hughes
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - B Vojtkova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - J Anand
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - A Mihut
- Department of Biology, University of York, York, UK
| | - P B Walrad
- York Biomedical Research Institute, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - L G Wilson
- York Biomedical Research Institute, University of York, York, UK
- Department of Physics, University of York, York, UK
| | - J W Pitchford
- Department of Biology, University of York, York, UK
- Department of Mathematics, University of York, York, UK
| | - P Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - J C Mottram
- York Biomedical Research Institute, University of York, York, UK.
- Department of Biology, University of York, York, UK.
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19
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Correa-Sáez A, Jiménez-Izquierdo R, Garrido-Rodríguez M, Morrugares R, Muñoz E, Calzado MA. Updating dual-specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2): molecular basis, functions and role in diseases. Cell Mol Life Sci 2020; 77:4747-4763. [PMID: 32462403 PMCID: PMC7658070 DOI: 10.1007/s00018-020-03556-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022]
Abstract
Members of the dual-specificity tyrosine-regulated kinase (DYRKs) subfamily possess a distinctive capacity to phosphorylate tyrosine, serine, and threonine residues. Among the DYRK class II members, DYRK2 is considered a unique protein due to its role in disease. According to the post-transcriptional and post-translational modifications, DYRK2 expression greatly differs among human tissues. Regarding its mechanism of action, this kinase performs direct phosphorylation on its substrates or acts as a priming kinase, enabling subsequent substrate phosphorylation by GSK3β. Moreover, DYRK2 acts as a scaffold for the EDVP E3 ligase complex during the G2/M phase of cell cycle. DYRK2 functions such as cell survival, cell development, cell differentiation, proteasome regulation, and microtubules were studied in complete detail in this review. We have also gathered available information from different bioinformatic resources to show DYRK2 interactome, normal and tumoral tissue expression, and recurrent cancer mutations. Then, here we present an innovative approach to clarify DYRK2 functionality and importance. DYRK2 roles in diseases have been studied in detail, highlighting this kinase as a key protein in cancer development. First, DYRK2 regulation of c-Jun, c-Myc, Rpt3, TERT, and katanin p60 reveals the implication of this kinase in cell-cycle-mediated cancer development. Additionally, depletion of this kinase correlated with reduced apoptosis, with consequences on cancer patient response to chemotherapy. Other functions like cancer stem cell formation and epithelial-mesenchymal transition regulation are also controlled by DYRK2. Furthermore, the pharmacological modulation of this protein by different inhibitors (harmine, curcumine, LDN192960, and ID-8) has enabled to clarify DYRK2 functionality.
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Affiliation(s)
- Alejandro Correa-Sáez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Avda. Menéndez Pidal s/n., 14004, Córdoba, Spain
- Departamento de Biología Celular, Fisiología E Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Rafael Jiménez-Izquierdo
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Avda. Menéndez Pidal s/n., 14004, Córdoba, Spain
- Departamento de Biología Celular, Fisiología E Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Martín Garrido-Rodríguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Avda. Menéndez Pidal s/n., 14004, Córdoba, Spain
- Departamento de Biología Celular, Fisiología E Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Rosario Morrugares
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Avda. Menéndez Pidal s/n., 14004, Córdoba, Spain
- Departamento de Biología Celular, Fisiología E Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Eduardo Muñoz
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Avda. Menéndez Pidal s/n., 14004, Córdoba, Spain
- Departamento de Biología Celular, Fisiología E Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Marco A Calzado
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Avda. Menéndez Pidal s/n., 14004, Córdoba, Spain.
- Departamento de Biología Celular, Fisiología E Inmunología, Universidad de Córdoba, Córdoba, Spain.
- Hospital Universitario Reina Sofía, Córdoba, Spain.
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20
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Cayla M, Matthews KR, Ivens AC. A global analysis of low-complexity regions in the Trypanosoma brucei proteome reveals enrichment in the C-terminus of nucleic acid binding proteins providing potential targets of phosphorylation. Wellcome Open Res 2020; 5:219. [PMID: 33274300 PMCID: PMC7682498 DOI: 10.12688/wellcomeopenres.16286.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2020] [Indexed: 11/29/2022] Open
Abstract
Background: Low-complexity regions (LCRs) on proteins have attracted increasing attention recently due to their role in the assembly of membraneless organelles or granules by liquid-liquid phase separation. Several examples of such granules have been shown to sequester RNA and proteins in an inactive state, providing an important mechanism for dynamic post-transcriptional gene regulation. In trypanosome parasites, post-transcriptional control overwhelmingly dominates gene regulation due to the organisation of their genome into polycistronic transcription units. The purpose of the current study was to generate a substantially more comprehensive genome-wide survey of LCRs on trypanosome proteins than currently available . Methods: Using the Shannon's entropy method, provided in the R package 'entropy', we identified LCRs in the proteome of Trypanosoma brucei. Our analysis predicts LCRs and their positional enrichment in distinct protein cohorts and superimposes on this a range of post-translational modifications derived from available experimental datasets. Results: We have identified 8162 LCRs present on 4914 proteins, representing 42% of the proteome, placing Trypanosoma brucei among the eukaryotes with the highest percentage of LCRs . Our results highlight the enrichment of LCRs in the C-terminal region of predicted nucleic acid binding proteins, these acting as favoured sites for potential phosphorylation. Phosphorylation represents 51% of the post-translational modifications present on LCRs compared to 16% on the rest of the proteome. Conclusions: The post-translational modifications of LCRs, and in particular phosphorylation events, could contribute to post-transcriptional gene expression control and the dynamics of protein targeting to membraneless organelles in kinetoplastid parasites.
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Affiliation(s)
- Mathieu Cayla
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3JT, UK
| | - Keith R. Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3JT, UK
| | - Alasdair C. Ivens
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3JT, UK
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21
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Cayla M, Matthews KR, Ivens AC. A global analysis of low-complexity regions in the Trypanosoma brucei proteome reveals enrichment in the C-terminus of nucleic acid binding proteins providing potential targets of phosphorylation. Wellcome Open Res 2020; 5:219. [PMID: 33274300 PMCID: PMC7682498 DOI: 10.12688/wellcomeopenres.16286.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 03/31/2024] Open
Abstract
Background: Low-complexity regions (LCRs) on proteins have attracted increasing attention recently due to their role in the assembly of membraneless organelles or granules by liquid-liquid phase separation. Several examples of such granules have been shown to sequester RNA and proteins in an inactive state, providing an important mechanism for dynamic post-transcriptional gene regulation. In trypanosome parasites, post-transcriptional control overwhelmingly dominates gene regulation due to the organisation of their genome into polycistronic transcription units. The purpose of the current study was to generate a substantially more comprehensive genome-wide survey of LCRs on trypanosome proteins than currently available . Methods: Using the Shannon's entropy method, provided in the R package 'entropy', we identified LCRs in the proteome of Trypanosoma brucei. Our analysis predicts LCRs and their positional enrichment in distinct protein cohorts and superimposes on this a range of post-translational modifications derived from available experimental datasets. Results: Our results highlight the enrichment of LCRs in the C-terminal region of predicted nucleic acid binding proteins, these acting as favoured sites for potential phosphorylation. Conclusions: The post-translational modifications of LCRs, and in particular the phosphorylation events, could contribute to post-transcriptional gene expression control and the dynamics of protein targeting to membraneless organelles in kinetoplastid parasites.
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Affiliation(s)
- Mathieu Cayla
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3JT, UK
| | - Keith R. Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3JT, UK
| | - Alasdair C. Ivens
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, EH9 3JT, UK
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