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Bard JE, Tylec BL, Dubey AP, Lamb NA, Yergeau DA, Read LK. Life stage-specific poly(A) site selection regulated by Trypanosoma brucei DRBD18. Proc Natl Acad Sci U S A 2024; 121:e2403188121. [PMID: 38990950 PMCID: PMC11260167 DOI: 10.1073/pnas.2403188121] [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: 02/21/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024] Open
Abstract
The kinetoplastid parasite, Trypanosoma brucei, undergoes a complex life cycle entailing slender and stumpy bloodstream forms in mammals and procyclic and metacyclic forms (MFs) in tsetse fly hosts. The numerous gene regulatory events that underlie T. brucei differentiation between hosts, as well as between active and quiescent stages within each host, take place in the near absence of transcriptional control. Rather, differentiation is controlled by RNA-binding proteins (RBPs) that associate with mRNA 3' untranslated regions (3'UTRs) to impact RNA stability and translational efficiency. DRBD18 is a multifunctional T. brucei RBP, shown to impact mRNA stability, translation, export, and processing. Here, we use single-cell RNAseq to characterize transcriptomic changes in cell populations that arise upon DRBD18 depletion, as well as to visualize transcriptome-wide alterations to 3'UTR length. We show that in procyclic insect stages, DRBD18 represses expression of stumpy bloodstream form and MF transcripts. Additionally, DRBD18 regulates the 3'UTR lengths of over 1,500 transcripts, typically promoting the use of distal polyadenylation sites, and thus the inclusion of 3'UTR regulatory elements. Remarkably, comparison of polyadenylation patterns in DRBD18 knockdowns with polyadenylation patterns in stumpy bloodstream forms shows numerous similarities, revealing a role for poly(A) site selection in developmental gene regulation, and indicating that DRBD18 controls this process for a set of transcripts. RNA immunoprecipitation supports a direct role for DRBD18 in poly(A) site selection. This report highlights the importance of alternative polyadenylation in T. brucei developmental control and identifies a critical RBP in this process.
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Affiliation(s)
- Jonathan E. Bard
- Genomics and Bioinformatics Core, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
- Department of Biochemistry, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Brianna L. Tylec
- Department of Microbiology and Immunology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Ashutosh P. Dubey
- Department of Microbiology and Immunology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Natalie A. Lamb
- Genomics and Bioinformatics Core, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Donald A. Yergeau
- Genomics and Bioinformatics Core, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
| | - Laurie K. Read
- Department of Microbiology and Immunology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY14203
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2
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Niemirowicz GT, Carlevaro G, Campetella O, Bouvier LA, Mucci J. A versatile 2A peptide-based strategy for ectopic expression and endogenous gene tagging in Trypanosoma cruzi. Heliyon 2024; 10:e24595. [PMID: 38304823 PMCID: PMC10830525 DOI: 10.1016/j.heliyon.2024.e24595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Nearly all expression vectors currently available for Trypanosoma cruzi were conceived to produce a single primary transcript containing the genes of interest along with those that confer antibiotic resistance. However, since each messenger RNA (mRNA) matures separately, drug selection will only guarantee the expression of those derived from the selectable marker. Therefore, commonly a considerable fraction of the cells recovered after selection with these expression vectors, although resistant do not express the protein of interest. Consequently, in order to counteract this disadvantage, we developed vectors with an alternative arrangement in which the gene of interest and antibiotic resistance are fused sharing the same mRNA. To test this configuration, we included the coding sequence for the green fluorescent protein (mEGFP) linked to the one conferring neomycin resistance (Neo). Additionally, to allow for the production of two independent proteins the sequence for a Thosea asigna virus self-cleaving 2A peptide (T2A) was inserted in-between. Cells obtained with these vectors displayed higher mEGFP expression levels with more homogeneous transgenic parasite populations than those transfected with more conventional independent mRNA-based alternatives. Moreover, as determined by Western blot, 2A mediated fusion protein dissociation occurred with high efficiency in all parasite stages. In addition, these vectors could easily be transformed into endogenous tagging constructs that allowed the insertion, by ends-in homologous recombination, of a hemagglutinin tag (HA) fused to the actin gene. The use of 2A self-cleaving peptides in the context of single mRNA vectors represents an interesting strategy capable of improving ectopic transgene expression in T. cruzi as well as providing a simple alternative to more sophisticated methods, such as the one based on CRISPR/Cas9, for the endogenous labeling of genes.
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Affiliation(s)
| | | | - Oscar Campetella
- Instituto de Investigaciones Biotecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Universidad Nacional de San Martín–Escuela de Bio y Nanotecnologías (EByN). Campus Miguelete, 25 de Mayo y Francia (B1650HMP), San Martín, Argentina
| | - León A. Bouvier
- Instituto de Investigaciones Biotecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Universidad Nacional de San Martín–Escuela de Bio y Nanotecnologías (EByN). Campus Miguelete, 25 de Mayo y Francia (B1650HMP), San Martín, Argentina
| | - Juan Mucci
- Instituto de Investigaciones Biotecnológicas, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Universidad Nacional de San Martín–Escuela de Bio y Nanotecnologías (EByN). Campus Miguelete, 25 de Mayo y Francia (B1650HMP), San Martín, Argentina
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3
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Díaz-Viraqué F, Chiribao ML, Libisch MG, Robello C. Genome-wide chromatin interaction map for Trypanosoma cruzi. Nat Microbiol 2023; 8:2103-2114. [PMID: 37828247 PMCID: PMC10627812 DOI: 10.1038/s41564-023-01483-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/25/2023] [Indexed: 10/14/2023]
Abstract
Trypanosomes are eukaryotic, unicellular parasites, such as Trypanosoma brucei, which causes sleeping sickness, and Trypanosoma cruzi, which causes Chagas disease. Genomes of these parasites comprise core regions and species-specific disruptive regions that encode multigene families of surface glycoproteins. Few transcriptional regulators have been identified in these parasites, and the role of spatial organization of the genome in gene expression is unclear. Here we mapped genome-wide chromatin interactions in T. cruzi using chromosome conformation capture (Hi-C), and we show that the core and disruptive regions form three-dimensional chromatin compartments named C and D. These chromatin compartments differ in levels of DNA methylation, nucleosome positioning and chromatin interactions, affecting genome expression dynamics. Our data reveal that the trypanosome genome is organized into chromatin-folding domains and transcription is affected by the local chromatin structure. We propose a model in which epigenetic mechanisms affect gene expression in trypanosomes.
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Affiliation(s)
- Florencia Díaz-Viraqué
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María Laura Chiribao
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - María Gabriela Libisch
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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4
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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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Kamran M, Bhattacharjee R, Das S, Mukherjee S, Ali N. The paradigm of intracellular parasite survival and drug resistance in leishmanial parasite through genome plasticity and epigenetics: Perception and future perspective. Front Cell Infect Microbiol 2023; 13:1001973. [PMID: 36814446 PMCID: PMC9939536 DOI: 10.3389/fcimb.2023.1001973] [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] [Received: 07/24/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Leishmania is an intracellular, zoonotic, kinetoplastid eukaryote with more than 1.2 million cases all over the world. The leishmanial chromosomes are divided into polymorphic chromosomal ends, conserved central domains, and antigen-encoding genes found in telomere-proximal regions. The genome flexibility of chromosomal ends of the leishmanial parasite is known to cause drug resistance and intracellular survival through the evasion of host defense mechanisms. Therefore, in this review, we discuss the plasticity of Leishmania genome organization which is the primary cause of drug resistance and parasite survival. Moreover, we have not only elucidated the causes of such genome plasticity which includes aneuploidy, epigenetic factors, copy number variation (CNV), and post-translation modification (PTM) but also highlighted their impact on drug resistance and parasite survival.
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Affiliation(s)
| | | | - Sonali Das
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Sohitri Mukherjee
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
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Sequences and proteins that influence mRNA processing in Trypanosoma brucei: Evolutionary conservation of SR-domain and PTB protein functions. PLoS Negl Trop Dis 2022; 16:e0010876. [PMID: 36288402 PMCID: PMC9639853 DOI: 10.1371/journal.pntd.0010876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/07/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Spliced leader trans splicing is the addition of a short, capped sequence to the 5' end of mRNAs. It is widespread in eukaryotic evolution, but factors that influence trans splicing acceptor site choice have been little investigated. In Kinetoplastids, all protein-coding mRNAs are 5' trans spliced. A polypyrimidine tract is usually found upstream of the AG splice acceptor, but there is no branch point consensus; moreover, splicing dictates polyadenylation of the preceding mRNA, which is a validated drug target. METHODOLOGY AND PRINCIPAL FINDINGS We here describe a trans splicing reporter system that can be used for studies and screens concerning the roles of sequences and proteins in processing site choice and efficiency. Splicing was poor with poly(U) tracts less than 9 nt long, and was influenced by an intergenic region secondary structure. A screen for signals resulted in selection of sequences that were on average 45% U and 35% C. Tethering of either the splicing factor SF1, or the cleavage and polyadenylation factor CPSF3 within the intron stimulated processing in the correct positions, while tethering of two possible homologues of Opisthokont PTB inhibited processing. In contrast, tethering of SR-domain proteins RBSR1, RBSR2, or TSR1 or its interaction partner TSR1IP, promoted use of alternative signals upstream of the tethering sites. RBSR1 interacts predominantly with proteins implicated in splicing, whereas the interactome of RBSR2 is more diverse. CONCLUSIONS Our selectable constructs are suitable for screens of both sequences, and proteins that affect mRNA processing in T. brucei. Our results suggest that the functions of PTB and SR-domain proteins in splice site definition may already have been present in the last eukaryotic common ancestor.
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Bishola Tshitenge T, Clayton C. The Trypanosoma brucei RNA-binding protein DRBD18 ensures correct mRNA trans splicing and polyadenylation patterns. RNA (NEW YORK, N.Y.) 2022; 28:1239-1262. [PMID: 35793904 PMCID: PMC9380746 DOI: 10.1261/rna.079258.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The parasite Trypanosoma brucei grows as bloodstream forms in mammals, and as procyclic forms in tsetse flies. Transcription is polycistronic, all mRNAs are trans spliced, and polyadenylation sites are defined by downstream splicing signals. Expression regulation therefore depends heavily on post-transcriptional mechanisms. The RNA-binding protein DRBD18 was previously implicated in the export of some mRNAs from the nucleus in procyclic forms. It copurifies the outer ring of the nuclear pore, mRNA export factors and exon-junction-complex proteins. We show that for more than 200 mRNAs, DRBD18 depletion caused preferential accumulation of versions with shortened 3'-untranslated regions, arising from use of polyadenylation sites that were either undetectable or rarely seen in nondepleted cells. The shortened mRNAs were often, but not always, more abundant in depleted cells than the corresponding longer versions in normal cells. Their appearance was linked to the appearance of trans-spliced, polyadenylated RNAs containing only downstream 3'-untranslated region-derived sequences. Experiments with one mRNA suggested that nuclear retention alone, through depletion of MEX67, did not affect mRNA length, suggesting a specific effect of DRBD18 on processing. DRBD18-bound mRNAs were enriched in polypyrimidine tract motifs, and DRBD18 was found in both the nucleus and the cytoplasm. We therefore suggest that in the nucleus, DRBD18 might bind to polypyrimidine tracts in 3'-UTRs of mRNA precursors. Such binding might both prevent recognition of mRNA-internal polypyrimidine tracts by splicing factors, and promote export of the processed bound mRNAs to the cytosol.
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Affiliation(s)
| | - Christine Clayton
- Heidelberg University Center for Molecular Biology (ZMBH), D69120 Heidelberg, Germany
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8
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Budzak J, Rudenko G. Pedal to the Metal: Nuclear Splicing Bodies Turbo-Charge VSG mRNA Production in African Trypanosomes. Front Cell Dev Biol 2022; 10:876701. [PMID: 35517511 PMCID: PMC9065277 DOI: 10.3389/fcell.2022.876701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/18/2022] [Indexed: 11/18/2022] Open
Abstract
The African trypanosome Trypanosoma brucei is a parasite of the mammalian bloodstream and tissues, where an antigenically variable Variant Surface Glycoprotein (VSG) coat protects it from immune attack. This dense layer comprised of ∼107 VSG proteins, makes VSG by far the most abundant mRNA (7-10% total) and protein (∼10% total) in the bloodstream form trypanosome. How can such prodigious amounts of VSG be produced from a single VSG gene? Extremely high levels of RNA polymerase I (Pol I) transcription of the active VSG provide part of the explanation. However, recent discoveries highlight the role of pre-mRNA processing, both in maintaining high levels of VSG transcription, as well as its monoallelic expression. Trypanosome mRNAs are matured through trans-splicing a spliced leader (SL) RNA to the 5' end of precursor transcripts, meaning abundant SL RNA is required throughout the nucleus. However, requirement for SL RNA in the vicinity of the active VSG gene is so intense, that the cell reconfigures its chromatin architecture to facilitate interaction between the SL RNA genes and the active VSG. This presumably ensures that sufficient localised SL RNA is available, and not limiting for VSG mRNA expression. Recently, novel nuclear splicing bodies which appear to provide essential trans-splicing components, have been identified associating with the active VSG. These observations highlight the underappreciated role of pre-mRNA processing in modulating gene expression in trypanosomes. Dissecting the function of these nuclear RNA processing bodies should help us elucidate the mechanisms of both VSG expression and monoallelic exclusion in T. brucei.
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Affiliation(s)
| | - Gloria Rudenko
- Department of Life Sciences, Sir Alexander Fleming Building, Imperial College London, London, United Kingdom
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9
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Cordon-Obras C, Gomez-Liñan C, Torres-Rusillo S, Vidal-Cobo I, Lopez-Farfan D, Barroso-Del Jesus A, Rojas-Barros D, Carrington M, Navarro M. Identification of sequence-specific promoters driving polycistronic transcription initiation by RNA polymerase II in trypanosomes. Cell Rep 2022; 38:110221. [PMID: 35021094 DOI: 10.1016/j.celrep.2021.110221] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 11/20/2022] Open
Abstract
Protein-coding genes in trypanosomes occur in polycistronic transcription units (PTUs). How RNA polymerase II (Pol II) initiates transcription of PTUs has not been resolved; the current model favors chromatin modifications inducing transcription rather than sequence-specific promoters. Here, we uncover core promoters by functional characterization of Pol II peaks identified by chromatin immunoprecipitation sequencing (ChIP-seq). Two distinct promoters are located between divergent PTUs, each driving unidirectional transcription. Detailed analysis identifies a 75-bp promoter that is necessary and sufficient to drive full reporter expression and contains functional motifs. Analysis of further promoters suggests transcription initiation is regulated and promoters are either focused or dispersed. In contrast to the previous model of unregulated and promoter-independent transcription initiation, we find that sequence-specific promoters determine the initiation of Pol II transcription of protein-coding genes PTUs. These findings in Trypanosoma brucei suggest that in addition of chromatin modifications, promoter motifs-based regulation of gene expression is deeply conserved among eukaryotes.
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Affiliation(s)
- Carlos Cordon-Obras
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Claudia Gomez-Liñan
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Sara Torres-Rusillo
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Isabel Vidal-Cobo
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Diana Lopez-Farfan
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Alicia Barroso-Del Jesus
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Domingo Rojas-Barros
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina López Neyra, Consejo Superior de Investigaciones Científicas, IPBLN-CSIC, 18016 Granada, Spain.
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Staneva DP, Bresson S, Auchynnikava T, Spanos C, Rappsilber J, Jeyaprakash AA, Tollervey D, Matthews KR, Allshire RC. The SPARC complex defines RNAPII promoters in Trypanosoma brucei. eLife 2022; 11:83135. [PMID: 36169304 PMCID: PMC9566855 DOI: 10.7554/elife.83135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/27/2022] [Indexed: 11/15/2022] Open
Abstract
Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodomain protein CRD1 are tightly concentrated at RNAPII transcription start regions (TSRs). Here, we report that SET27 and CRD1, together with four previously uncharacterized constituents, form the SET27 promoter-associated regulatory complex (SPARC), which is specifically enriched at TSRs. SET27 loss leads to aberrant RNAPII recruitment to promoter sites, accumulation of polyadenylated transcripts upstream of normal transcription start sites, and conversion of some normally unidirectional promoters to bidirectional promoters. Transcriptome analysis in the absence of SET27 revealed upregulated mRNA expression in the vicinity of SPARC peaks within the main body of chromosomes in addition to derepression of genes encoding variant surface glycoproteins (VSGs) located in subtelomeric regions. These analyses uncover a novel chromatin-associated complex required to establish accurate promoter position and directionality.
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Affiliation(s)
- Desislava P Staneva
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom,Institute of Immunology and Infection Biology, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Stefan Bresson
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
| | | | - Christos Spanos
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom,Institute of Biotechnology, Technische UniversitätBerlinGermany
| | | | - David Tollervey
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
| | - Keith R Matthews
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, University of EdinburghEdinburghUnited Kingdom
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Characterization of an Atypical eIF4E Ortholog in Leishmania, LeishIF4E-6. Int J Mol Sci 2021; 22:ijms222312720. [PMID: 34884522 PMCID: PMC8657474 DOI: 10.3390/ijms222312720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 01/11/2023] Open
Abstract
Leishmania parasites are digenetic protists that shuffle between sand fly vectors and mammalian hosts, transforming from flagellated extracellular promastigotes that reside within the intestinal tract of female sand flies to the obligatory intracellular and non-motile amastigotes within mammalian macrophages. Stage differentiation is regulated mainly by post-transcriptional mechanisms, including translation regulation. Leishmania parasites encode six different cap-binding proteins, LeishIF4E1-6, that show poor conservation with their counterparts from higher eukaryotes and among themselves. In view of the changing host milieu encountered throughout their life cycle, we propose that each LeishIF4E has a unique role, although these functions may be difficult to determine. Here we characterize LeishIF4E-6, a unique eIF4E ortholog that does not readily associate with m7GTP cap in either of the tested life forms of the parasite. We discuss the potential effect of substituting two essential tryptophan residues in the cap-binding pocket, expected to be involved in the cap-binding activity, as judged from structural studies in the mammalian eIF4E. LeishIF4E-6 binds to LeishIF4G-5, one of the five eIF4G candidates in Leishmania. However, despite this binding, LeishIF4E-6 does not appear to function as a translation factor. Its episomal overexpression causes a general reduction in the global activity of protein synthesis, which was not observed in the hemizygous deletion mutant generated by CRISPR-Cas9. This genetic profile suggests that LeishIF4E-6 has a repressive role. The interactome of LeishIF4E-6 highlights proteins involved in RNA metabolism such as the P-body marker DHH1, PUF1 and an mRNA-decapping enzyme that is homologous to the TbALPH1.
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12
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Salloum T, Tokajian S, Hirt RP. Advances in Understanding Leishmania Pathobiology: What Does RNA-Seq Tell Us? Front Cell Dev Biol 2021; 9:702240. [PMID: 34540827 PMCID: PMC8440825 DOI: 10.3389/fcell.2021.702240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a vector-borne disease caused by a protozoa parasite from over 20 Leishmania species. The clinical manifestations and the outcome of the disease vary greatly. Global RNA sequencing (RNA-Seq) analyses emerged as a powerful technique to profile the changes in the transcriptome that occur in the Leishmania parasites and their infected host cells as the parasites progresses through their life cycle. Following the bite of a sandfly vector, Leishmania are transmitted to a mammalian host where neutrophils and macrophages are key cells mediating the interactions with the parasites and result in either the elimination the infection or contributing to its proliferation. This review focuses on RNA-Seq based transcriptomics analyses and summarizes the main findings derived from this technology. In doing so, we will highlight caveats in our understanding of the parasite's pathobiology and suggest novel directions for research, including integrating more recent data highlighting the role of the bacterial members of the sandfly gut microbiota and the mammalian host skin microbiota in their potential role in influencing the quantitative and qualitative aspects of leishmaniasis pathology.
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Affiliation(s)
- Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Robert P. Hirt
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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13
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Rajan KS, Adler K, Madmoni H, Peleg-Chen D, Cohen-Chalamish S, Doniger T, Galili B, Gerber D, Unger R, Tschudi C, Michaeli S. Pseudouridines on Trypanosoma brucei mRNAs are developmentally regulated: Implications to mRNA stability and protein binding. Mol Microbiol 2021; 116:808-826. [PMID: 34165831 DOI: 10.1111/mmi.14774] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/11/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022]
Abstract
The parasite Trypanosoma brucei cycles between an insect and a mammalian host and is the causative agent of sleeping sickness. Here, we performed high-throughput mapping of pseudouridines (Ψs) on mRNA from two life stages of the parasite. The analysis revealed ~273 Ψs, including developmentally regulated Ψs that are guided by homologs of pseudouridine synthases (PUS1, 3, 5, and 7). Mutating the U that undergoes pseudouridylation in the 3' UTR of valyl-tRNA synthetase destabilized the mRNA level. To investigate the mechanism by which Ψ affects the stability of this mRNA, proteins that bind to the 3' UTR were identified, including the RNA binding protein RBSR1. The binding of RBSR1 protein to the 3' UTR was stronger when lacking Ψ compared to transcripts carrying the modification, suggesting that Ψ can inhibit the binding of proteins to their target and thus affect the stability of mRNAs. Consequently, Ψ modification on mRNA adds an additional level of regulation to the dominant post-transcriptional control in these parasites.
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Affiliation(s)
- K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Katerina Adler
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Hava Madmoni
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Dana Peleg-Chen
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Beathrice Galili
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
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14
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Kramer S, Meyer-Natus E, Stigloher C, Thoma H, Schnaufer A, Engstler M. Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples. Nucleic Acids Res 2021; 49:e14. [PMID: 33275141 PMCID: PMC7897490 DOI: 10.1093/nar/gkaa1142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 01/19/2023] Open
Abstract
Single mRNA molecules are frequently detected by single molecule fluorescence in situ hybridization (smFISH) using branched DNA technology. While providing strong and background-reduced signals, the method is inefficient in detecting mRNAs within dense structures, in monitoring mRNA compactness and in quantifying abundant mRNAs. To overcome these limitations, we have hybridized slices of high pressure frozen, freeze-substituted and LR White embedded cells (LR White smFISH). mRNA detection is physically restricted to the surface of the resin. This enables single molecule detection of RNAs with accuracy comparable to RNA sequencing, irrespective of their abundance, while at the same time providing spatial information on RNA localization that can be complemented with immunofluorescence and electron microscopy, as well as array tomography. Moreover, LR White embedding restricts the number of available probe pair recognition sites for each mRNA to a small subset. As a consequence, differences in signal intensities between RNA populations reflect differences in RNA structures, and we show that the method can be employed to determine mRNA compactness. We apply the method to answer some outstanding questions related to trans-splicing, RNA granules and mitochondrial RNA editing in single-cellular trypanosomes and we show an example of differential gene expression in the metazoan Caenorhabditis elegans.
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Affiliation(s)
- Susanne Kramer
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | | | - Christian Stigloher
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany.,Imaging Core Facility, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Hanna Thoma
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Achim Schnaufer
- Institute for Immunology & Infection Research, University of Edinburgh, Edinburgh, UK
| | - Markus Engstler
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
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15
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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16
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Barbosa RL, da Cunha JPC, Menezes AT, Melo RDFP, Elias MC, Silber AM, Coltri PP. Proteomic analysis of Trypanosoma cruzi spliceosome complex. J Proteomics 2020; 223:103822. [PMID: 32422275 DOI: 10.1016/j.jprot.2020.103822] [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: 11/29/2019] [Revised: 05/01/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022]
Abstract
The unicellular protists of the group Kinetoplastida include the genera Leishmania and Trypanosoma, which are pathogens of invertebrate and vertebrate animals. Despite their medical and economical importance, critical aspects of their biology such as specific molecular characteristics of gene expression regulation are just beginning to be deciphered. Gene expression regulation also depends on post-transcriptional processing steps, such as the trans-splicing process. Despite being widely used in trypanosomes, trans-splicing is a rare event in other eukaryotes. We sought to describe the protein composition of spliceosomes in epimastigotes of T. cruzi, the etiological agent of Chagas disease. We used two TAP-tagged proteins to affinity purify spliceosomes and analyzed their composition by mass spectrometry. Among the 115 identified proteins we detected conserved spliceosome components, as Sm and LSm proteins, RNA helicases, U2- and U5-snRNP specific proteins. Importantly, by comparing our data with proteomic data of human and T. brucei spliceosome complexes, we observed a core group of proteins common to all spliceosomes. By using amino acid sequence comparisons, we identified RNA-associated proteins that might be involved with splicing regulation in T. cruzi, namely the orthologous of WDR33, PABPCL1 and three different HNRNPs. Data are available via ProteomeXchange with identifier PXD018776.
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Affiliation(s)
- Rosicler L Barbosa
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Arthur T Menezes
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Raíssa de F P Melo
- Laboratory of Biochemistry of Tryps - LaBTryps. Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Maria Carolina Elias
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Ariel M Silber
- Laboratory of Biochemistry of Tryps - LaBTryps. Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil.
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17
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Gosavi U, Srivastava A, Badjatia N, Günzl A. Rapid block of pre-mRNA splicing by chemical inhibition of analog-sensitive CRK9 in Trypanosoma brucei. Mol Microbiol 2020; 113:1225-1239. [PMID: 32068297 PMCID: PMC7299817 DOI: 10.1111/mmi.14489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/24/2022]
Abstract
Trypanosoma brucei CRK9 is an essential cyclin-dependent kinase for the parasite-specific mode of pre-mRNA processing. In trypanosomes, protein coding genes are arranged in directional arrays that are transcribed polycistronically, and individual mRNAs are generated by spliced leader trans-splicing and polyadenylation, processes that are functionally linked. Since CRK9 silencing caused a decline of mRNAs, a concomitant increase of unspliced pre-mRNAs and the disappearance of the trans-splicing Y structure intermediate, CRK9 is essential for the first step of splicing. CRK9 depletion also caused a loss of phosphorylation in RPB1, the largest subunit of RNA polymerase (pol) II. Here, we established cell lines that exclusively express analog-sensitive CRK9 (CRK9AS ). Inhibition of CRK9AS in these cells by the ATP-competitive inhibitor 1-NM-PP1 reproduced the splicing defects and proved that it is the CKR9 kinase activity that is required for pre-mRNA processing. Since defective trans-splicing was detected as early as 5 min after inhibitor addition, CRK9 presumably carries out reversible phosphorylation on the pre-mRNA processing machinery. Loss of RPB1 phosphorylation, however, took 12-24 hr. Surprisingly, RNA pol II-mediated RNA synthesis in 24 hr-treated cells was upregulated, indicating that, in contrast to other eukaryotes, RPB1 phosphorylation is not a prerequisite for transcription in trypanosomes.
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Affiliation(s)
- Ujwala Gosavi
- Department of Genetics and Genome Sciences, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Ankita Srivastava
- Department of Genetics and Genome Sciences, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Nitika Badjatia
- Department of Genetics and Genome Sciences, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
- Current address: Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Arthur Günzl
- Department of Genetics and Genome Sciences, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
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18
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Florini F, Naguleswaran A, Gharib WH, Bringaud F, Roditi I. Unexpected diversity in eukaryotic transcription revealed by the retrotransposon hotspot family of Trypanosoma brucei. Nucleic Acids Res 2019; 47:1725-1739. [PMID: 30544263 PMCID: PMC6393297 DOI: 10.1093/nar/gky1255] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/28/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
The path from DNA to RNA to protein in eukaryotes is guided by a series of factors linking transcription, mRNA export and translation. Many of these are conserved from yeast to humans. Trypanosomatids, which diverged early in the eukaryotic lineage, exhibit unusual features such as polycistronic transcription and trans-splicing of all messenger RNAs. They possess basal transcription factors, but lack recognisable orthologues of many factors required for transcription elongation and mRNA export. We show that retrotransposon hotspot (RHS) proteins fulfil some of these functions and that their depletion globally impairs nascent RNA synthesis by RNA polymerase II. Three sub-families are part of a coordinated process in which RHS6 is most closely associated with chromatin, RHS4 is part of the Pol II complex and RHS2 connects transcription with the translation machinery. In summary, our results show that the components of eukaryotic transcription are far from being universal, and reveal unsuspected plasticity in the course of evolution.
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Affiliation(s)
- Francesca Florini
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Science, University of Bern, Bern, Switzerland
| | | | - Walid H Gharib
- Interfaculty Bioinformatics Unit, University of Bern, Switzerland
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234 CNRS, Université de Bordeaux, France
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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19
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Briggs E, Hamilton G, Crouch K, Lapsley C, McCulloch R. Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome. Nucleic Acids Res 2018; 46:11789-11805. [PMID: 30304482 PMCID: PMC6294496 DOI: 10.1093/nar/gky928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/25/2018] [Accepted: 10/05/2018] [Indexed: 01/09/2023] Open
Abstract
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localization was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the regions between coding sequences of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination the most widespread localization of R-loops in T. brucei suggests a novel correlation with pre-mRNA processing. Finally, we find little evidence for correlation between R-loop localization and mapped sites of DNA replication initiation.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Rd, Bearsden, G61 1QH, UK
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
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20
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Niemirowicz GT, Cazzulo JJ, Álvarez VE, Bouvier LA. Simplified inducible system for Trypanosoma brucei. PLoS One 2018; 13:e0205527. [PMID: 30308039 PMCID: PMC6181392 DOI: 10.1371/journal.pone.0205527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/26/2018] [Indexed: 11/18/2022] Open
Abstract
Nowadays, most reverse genetics approaches in Trypanosoma brucei, a protozoan parasite of medical and veterinary importance, rely on pre-established cell lines. Consequently, inducible experimentation is reduced to a few laboratory strains. Here we described a new transgene expression system based exclusively on endogenous transcription activities and a minimum set of regulatory components that can easily been adapted to different strains. The pTbFIX vectors are designed to contain the sequence of interest under the control of an inducible rRNA promoter along with a constitutive dicistronic unit encoding a nucleus targeted tetracycline repressor and puromycin resistance genes in a tandem “head-to-tail” configuration. Upon doxycycline induction, the system supports regulatable GFP expression (170 to 400 fold) in both bloodstream and procyclic T. brucei forms. Furthermore we have adapted the pTbFIX plasmid to perform RNAi experimentation. Lethal phenotypes, including α-tubulin and those corresponding to the enolase and clathrin heavy chain genes, were successfully recapitulated in procyclic and bloodstream parasites thus showing the versatility of this new tool.
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Affiliation(s)
- Gabriela T. Niemirowicz
- Instituto de Investigaciones Biotecnológicas (IIB) Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Juan J. Cazzulo
- Instituto de Investigaciones Biotecnológicas (IIB) Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Vanina E. Álvarez
- Instituto de Investigaciones Biotecnológicas (IIB) Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - León A. Bouvier
- Instituto de Investigaciones Biotecnológicas (IIB) Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
- * E-mail:
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21
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Abstract
African trypanosomes cause lethal and neglected tropical diseases, known as sleeping sickness in humans and nagana in animals. Current therapies are limited, but fortunately, promising therapies are in advanced clinical and veterinary development, including acoziborole (AN5568 or SCYX-7158) and AN11736, respectively. These benzoxaboroles will likely be key to the World Health Organization's target of disease control by 2030. Their mode of action was previously unknown. We have developed a high-coverage overexpression library and use it here to explore drug mode of action in Trypanosoma brucei Initially, an inhibitor with a known target was used to select for drug resistance and to test massive parallel library screening and genome-wide mapping; this effectively identified the known target and validated the approach. Subsequently, the overexpression screening approach was used to identify the target of the benzoxaboroles, Cleavage and Polyadenylation Specificity Factor 3 (CPSF3, Tb927.4.1340). We validated the CPSF3 endonuclease as the target, using independent overexpression strains. Knockdown provided genetic validation of CPSF3 as essential, and GFP tagging confirmed the expected nuclear localization. Molecular docking and CRISPR-Cas9-based editing demonstrated how acoziborole can specifically block the active site and mRNA processing by parasite, but not host CPSF3. Thus, our findings provide both genetic and chemical validation for CPSF3 as an important drug target in trypanosomes and reveal inhibition of mRNA maturation as the mode of action of the trypanocidal benzoxaboroles. Understanding the mechanism of action of benzoxaborole-based therapies can assist development of improved therapies, as well as the prediction and monitoring of resistance, if or when it arises.
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22
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Begolo D, Vincent IM, Giordani F, Pöhner I, Witty MJ, Rowan TG, Bengaly Z, Gillingwater K, Freund Y, Wade RC, Barrett MP, Clayton C. The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing. PLoS Pathog 2018; 14:e1007315. [PMID: 30252911 PMCID: PMC6173450 DOI: 10.1371/journal.ppat.1007315] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/05/2018] [Accepted: 09/04/2018] [Indexed: 11/25/2022] Open
Abstract
Kinetoplastid parasites-trypanosomes and leishmanias-infect millions of humans and cause economically devastating diseases of livestock, and the few existing drugs have serious deficiencies. Benzoxaborole-based compounds are very promising potential novel anti-trypanosomal therapies, with candidates already in human and animal clinical trials. We investigated the mechanism of action of several benzoxaboroles, including AN7973, an early candidate for veterinary trypanosomosis. In all kinetoplastids, transcription is polycistronic. Individual mRNA 5'-ends are created by trans splicing of a short leader sequence, with coupled polyadenylation of the preceding mRNA. Treatment of Trypanosoma brucei with AN7973 inhibited trans splicing within 1h, as judged by loss of the Y-structure splicing intermediate, reduced levels of mRNA, and accumulation of peri-nuclear granules. Methylation of the spliced leader precursor RNA was not affected, but more prolonged AN7973 treatment caused an increase in S-adenosyl methionine and methylated lysine. Together, the results indicate that mRNA processing is a primary target of AN7973. Polyadenylation is required for kinetoplastid trans splicing, and the EC50 for AN7973 in T. brucei was increased three-fold by over-expression of the T. brucei cleavage and polyadenylation factor CPSF3, identifying CPSF3 as a potential molecular target. Molecular modeling results suggested that inhibition of CPSF3 by AN7973 is feasible. Our results thus chemically validate mRNA processing as a viable drug target in trypanosomes. Several other benzoxaboroles showed metabolomic and splicing effects that were similar to those of AN7973, identifying splicing inhibition as a common mode of action and suggesting that it might be linked to subsequent changes in methylated metabolites. Granule formation, splicing inhibition and resistance after CPSF3 expression did not, however, always correlate and prolonged selection of trypanosomes in AN7973 resulted in only 1.5-fold resistance. It is therefore possible that the modes of action of oxaboroles that target trypanosome mRNA processing might extend beyond CPSF3 inhibition.
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Affiliation(s)
- Daniela Begolo
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Isabel M. Vincent
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, 120 University Place, University of Glasgow, Glasgow, United Kingdom
| | - Federica Giordani
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, 120 University Place, University of Glasgow, Glasgow, United Kingdom
| | - Ina Pöhner
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg, Germany
| | - Michael J. Witty
- Global Alliance for Livestock and Veterinary Medicine, Doherty Building, Pentlands Science Park, Penicuik, Edinburgh, United Kingdom
| | - Timothy G. Rowan
- Global Alliance for Livestock and Veterinary Medicine, Doherty Building, Pentlands Science Park, Penicuik, Edinburgh, United Kingdom
| | - Zakaria Bengaly
- Centre International de Recherche–Développement sur l’Elevage en zone Subhumide (CIRDES), Bobo-Dioulasso 01, Burkina Faso
| | - Kirsten Gillingwater
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland
- University of Basel, Petersplatz 1, Basel, Switzerland
| | - Yvonne Freund
- Anacor Pharmaceuticals, Inc., Palo Alto, CA, United States of America
| | - Rebecca C. Wade
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg, Germany
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, 120 University Place, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Christine Clayton
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany
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23
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Zoltner M, Krienitz N, Field MC, Kramer S. Comparative proteomics of the two T. brucei PABPs suggests that PABP2 controls bulk mRNA. PLoS Negl Trop Dis 2018; 12:e0006679. [PMID: 30040867 PMCID: PMC6075789 DOI: 10.1371/journal.pntd.0006679] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 08/03/2018] [Accepted: 07/10/2018] [Indexed: 01/17/2023] Open
Abstract
Poly(A)-binding proteins (PABPs) regulate mRNA fate by controlling stability and translation through interactions with both the poly(A) tail and eIF4F complex. Many organisms have several paralogs of PABPs and eIF4F complex components and it is likely that different eIF4F/PABP complex combinations regulate distinct sets of mRNAs. Trypanosomes have five eIF4G paralogs, six of eIF4E and two PABPs, PABP1 and PABP2. Under starvation, polysomes dissociate and the majority of mRNAs, most translation initiation factors and PABP2 reversibly localise to starvation stress granules. To understand this more broadly we identified a protein interaction cohort for both T. brucei PABPs by cryo-mill/affinity purification-mass spectrometry. PABP1 very specifically interacts with the previously identified interactors eIF4E4 and eIF4G3 and few others. In contrast PABP2 is promiscuous, with a larger set of interactors including most translation initiation factors and most prominently eIF4G1, with its two partners TbG1-IP and TbG1-IP2. Only RBP23 was specific to PABP1, whilst 14 RNA-binding proteins were exclusively immunoprecipitated with PABP2. Significantly, PABP1 and associated proteins are largely excluded from starvation stress granules, but PABP2 and most interactors translocate to granules on starvation. We suggest that PABP1 regulates a small subpopulation of mainly small-sized mRNAs, as it interacts with a small and distinct set of proteins unable to enter the dominant pathway into starvation stress granules and localises preferentially to a subfraction of small polysomes. By contrast PABP2 likely regulates bulk mRNA translation, as it interacts with a wide range of proteins, enters stress granules and distributes over the full range of polysomes.
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Affiliation(s)
- Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nina Krienitz
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
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24
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Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 2018; 146:1-27. [PMID: 29898792 DOI: 10.1017/s0031182018000951] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental conditions, and omnipresence, these protists have major impact on all biotic communities that still needs to be fully elucidated. In addition, as these organisms represent a highly divergent evolutionary lineage, they are strikingly different from the common 'model system' eukaryotes, such as some mammals, plants or fungi. A number of excellent reviews, published over the past decade, were dedicated to specialized topics from the areas of trypanosomatid molecular and cell biology, biochemistry, host-parasite relationships or other aspects of these fascinating organisms. However, there is a need for a more comprehensive review that summarizing recent advances in the studies of trypanosomatids in the last 30 years, a task, which we tried to accomplish with the current paper.
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de Freitas Nascimento J, Kelly S, Sunter J, Carrington M. Codon choice directs constitutive mRNA levels in trypanosomes. eLife 2018; 7:e32467. [PMID: 29543152 PMCID: PMC5896880 DOI: 10.7554/elife.32467] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs. Third, translation was necessary for the accelerated mRNA turnover resulting from codon choice. Thus, in trypanosomes, the information determining the levels of most mRNAs resides in the open reading frame and translation is required to access this information.
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Affiliation(s)
| | - Steven Kelly
- Department of Plant SciencesUniversity of OxfordOxfordUnited Kingdom
| | - Jack Sunter
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Mark Carrington
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
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Wedel C, Förstner KU, Derr R, Siegel TN. GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes. EMBO J 2017; 36:2581-2594. [PMID: 28701485 PMCID: PMC5579346 DOI: 10.15252/embj.201695323] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/25/2023] Open
Abstract
Genome‐wide transcription studies are revealing an increasing number of “dispersed promoters” that, unlike “focused promoters”, lack well‐conserved sequence motifs and tight regulation. Dispersed promoters are nevertheless marked by well‐defined chromatin structures, suggesting that specific sequence elements must exist in these unregulated promoters. Here, we have analyzed regions of transcription initiation in the eukaryotic parasite Trypanosoma brucei, in which RNA polymerase II transcription initiation occurs over broad regions without distinct promoter motifs and lacks regulation. Using a combination of site‐specific and genome‐wide assays, we identified GT‐rich promoters that can drive transcription and promote the targeted deposition of the histone variant H2A.Z in a genomic context‐dependent manner. In addition, upon mapping nucleosome occupancy at high resolution, we find nucleosome positioning to correlate with RNA pol II enrichment and gene expression, pointing to a role in RNA maturation. Nucleosome positioning may thus represent a previously unrecognized layer of gene regulation in trypanosomes. Our findings show that even highly dispersed, unregulated promoters contain specific DNA elements that are able to induce transcription and changes in chromatin structure.
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Affiliation(s)
- Carolin Wedel
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany
| | | | - Ramona Derr
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany
| | - T Nicolai Siegel
- Research Center for Infectious Diseases, Universität Würzburg, Würzburg, Germany .,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, München, Germany.,Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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27
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De Pablos LM, Kelly S, de Freitas Nascimento J, Sunter J, Carrington M. Characterization of RBP9 and RBP10, two developmentally regulated RNA-binding proteins in Trypanosoma brucei. Open Biol 2017; 7:rsob.160159. [PMID: 28381627 PMCID: PMC5413900 DOI: 10.1098/rsob.160159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 03/08/2017] [Indexed: 12/19/2022] Open
Abstract
The fate of an mRNA is determined by its interaction with proteins and small RNAs within dynamic complexes called ribonucleoprotein complexes (mRNPs). In Trypanosoma brucei and related kinetoplastids, responses to internal and external signals are mainly mediated by post-transcriptional processes. Here, we used proximity-dependent biotin identification (BioID) combined with RNA-seq to investigate the changes resulting from ectopic expression of RBP10 and RBP9, two developmentally regulated RNA-binding proteins (RBPs). Both RBPs have reduced expression in insect procyclic forms (PCFs) compared with bloodstream forms (BSFs). Upon overexpression in PCFs, both proteins were recruited to cytoplasmic foci, co-localizing with the processing body marker SCD6. Further, both RBPs altered the transcriptome from a PCF- to a BSF-like pattern. Notably, upon expression of BirA*-RBP9 and BirA*-RBP10, BioID yielded more than 200 high confidence protein interactors (more than 10-fold enriched); 45 (RBP9) and 31 (RBP10) were directly related to mRNA metabolism. This study validates the use of BioID for investigating mRNP components but also illustrates the complexity of mRNP function.
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Affiliation(s)
- Luis Miguel De Pablos
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.,Centre for Immunology and Infection (CII). Biology Dept., University of York, York YO10 5DD, UK
| | - Steve Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | | | - Jack Sunter
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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28
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Maree JP, Povelones ML, Clark DJ, Rudenko G, Patterton HG. Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei. Epigenetics Chromatin 2017; 10:14. [PMID: 28344657 PMCID: PMC5359979 DOI: 10.1186/s13072-017-0121-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and mechanisms coevolved to regulate chromatin structure and its impact on DNA. This included the selection of specific nucleosome positions to modulate accessibility to the DNA molecule. Trypanosoma brucei, a member of the Excavates supergroup, falls in an ancient evolutionary branch of eukaryotes and provides valuable insight into the organization of chromatin in early genomes. Results We have mapped nucleosome positions in T. brucei and identified important differences compared to other eukaryotes: The RNA polymerase II initiation regions in T. brucei do not exhibit pronounced nucleosome depletion, and show little evidence for defined −1 and +1 nucleosomes. In contrast, a well-positioned nucleosome is present directly on the splice acceptor sites within the polycistronic transcription units. The RNA polyadenylation sites were depleted of nucleosomes, with a single well-positioned nucleosome present immediately downstream of the predicted sites. The regions flanking the silent variant surface glycoprotein (VSG) gene cassettes showed extensive arrays of well-positioned nucleosomes, which may repress cryptic transcription initiation. The silent VSG genes themselves exhibited a less regular nucleosomal pattern in both bloodstream and procyclic form trypanosomes. The DNA replication origins, when present within silent VSG gene cassettes, displayed a defined nucleosomal organization compared with replication origins in other chromosomal core regions. Conclusions Our results indicate that some organizational features of chromatin are evolutionarily ancient, and may already have been present in the last eukaryotic common ancestor. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0121-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Megan Lindsay Povelones
- Department of Biology, Pennsylvania State University (Brandywine Campus), Media, PA 19063 USA
| | - David Johannes Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Gloria Rudenko
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ UK
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Li K, Zhou S, Guo Q, Chen X, Lai DH, Lun ZR, Guo X. The eIF3 complex of Trypanosoma brucei: composition conservation does not imply the conservation of structural assembly and subunits function. RNA (NEW YORK, N.Y.) 2017; 23:333-345. [PMID: 27932584 PMCID: PMC5311491 DOI: 10.1261/rna.058651.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/24/2016] [Indexed: 05/03/2023]
Abstract
The multisubunit eukaryotic initiation factor 3 (eIF3) plays multiple roles in translation but is poorly understood in trypanosomes. The putative subunits eIF3a and eIF3f of Trypanosoma brucei (TbIF3a and TbIF3f) were overexpressed and purified, and 11 subunits were identified, TbIF3a through l minus j, which form a tight complex. Both TbIF3a and TbIF3f are essential for the viability of T. brucei RNAi knockdown of either of them severely reduced total translation and the ratio of the polysome/80S peak area. TbIF3f and TbIF3a RNAi cell lines were modified to express tagged-TbIF3a and -TbIF3f, respectively. RNAi in combination with affinity purification assays indicated that both subunits are variably required for TbIF3 stability and integrity. The relative abundance of other subunits in the TbIF3f-tag complex changed little upon TbIF3a depletion; while only subunits TbIF3b, i, and e copurified comparably with TbIF3a-tag upon TbIF3f depletion. A genome-wide UV-crosslinking assay showed that several TbIF3 subunits have direct RNA-binding activity, with TbIF3c showing the strongest signal. In addition, CrPV IRES, but neither EMCV IRES nor HCV IRES, was found to mediate translation in T. brucei These results together imply that the structure of TbIF3 and the subunits function have trypanosome-specific features, although the composition is evolutionarily conserved.
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Affiliation(s)
- Kunrao Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
| | - Shuru Zhou
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
| | - Qixuan Guo
- Chengde Nursing Vocational College, Chengde 067000, China
| | - Xin Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
| | - De-Hua Lai
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhao-Rong Lun
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xuemin Guo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China
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Bittencourt IDA, Serpeloni M, Hiraiwa PM, de Arruda Campos Brasil de Souza T, Ávila AR. Dissecting biochemical peculiarities of the ATPase activity of TcSub2, a component of the mRNA export pathway in Trypanosoma cruzi. Int J Biol Macromol 2017; 98:793-801. [PMID: 28212935 DOI: 10.1016/j.ijbiomac.2017.02.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 11/16/2022]
Abstract
The RNA helicase DEAD-box protein Sub2 (yeast)/UAP56 (mammals) is conserved across eukaryotes and is essential for mRNA export in trypanosomes. Despite the high conservation of Sub2 in lower eukaryotes such as Trypanosoma cruzi, the low conservation of other mRNA export factors raises questions regarding whether the mode of action of TcSub2 is similar to that of orthologs from other eukaryotes. Mutation of the conserved K87 residue of TcSub2 abolishes ATPase activity, showing that its ATPase domain is functional. However, the Vmax of TcSub2 was much higher than the Vmax described for the human protein UAP56, which suggests that the TcSub2 enzyme hydrolyzes ATP faster than its human homolog. Furthermore, we demonstrate that RNA association is less important to the activity of TcSub2 compared to UAP56. Our results show differences in activity of this protein, even though the structure of TcSub2 is very similar to UAP56. Functional complementation assays indicate that these differences may be common to other trypanosomatids. Distinct features of RNA influence and ATPase efficiency between UAP56 and TcSub2 may reflect distinct structures for functional sites of TcSub2. For this reason, ligand-based or structure-based methodologies can be applied to investigate the potential of TcSub2 as a target for new drugs.
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31
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Stiles JK, Hicock PI, Shah PH, Meade JC. Genomic organization, transcription, splicing and gene regulation inLeishmania. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 2016. [DOI: 10.1080/00034983.1999.11813485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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32
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Koch H, Raabe M, Urlaub H, Bindereif A, Preußer C. The polyadenylation complex of Trypanosoma brucei: Characterization of the functional poly(A) polymerase. RNA Biol 2016; 13:221-31. [PMID: 26727667 DOI: 10.1080/15476286.2015.1130208] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The generation of mature mRNA in the protozoan parasite Trypanosoma brucei requires coupled polyadenylation and trans splicing. In contrast to other eukaryotes, we still know very little on components, mechanisms, and dynamics of the 3' end-processing machinery in trypanosomes. To characterize the catalytic core of the polyadenylation complex in T. brucei, we first identified the poly(A) polymerase [Tb927.7.3780] as the major functional, nuclear-localized enzyme in trypanosomes. In contrast, another poly(A) polymerase, encoded by an intron-containing gene [Tb927.3.3160], localizes mainly in the cytoplasm and appears not to be functional in general 3' end processing of mRNAs. Based on tandem-affinity purification with tagged CPSF160 and mass spectrometry, we identified ten associated components of the trypanosome polyadenylation complex, including homologues to all four CPSF subunits, Fip1, CstF50/64, and Symplekin, as well as two hypothetical proteins. RNAi-mediated knockdown revealed that most of these factors are essential for growth and required for both in vivo polyadenylation and trans splicing, arguing for a general coupling of these two mRNA-processing reactions.
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Affiliation(s)
- Henrik Koch
- a Institute of Biochemistry, Justus Liebig University of Giessen , D-35392 Giessen , Germany
| | - Monika Raabe
- b Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry , D-37077 Göttingen , Germany
| | - Henning Urlaub
- b Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry , D-37077 Göttingen , Germany.,c Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen , D-37075 Göttingen , Germany
| | - Albrecht Bindereif
- a Institute of Biochemistry, Justus Liebig University of Giessen , D-35392 Giessen , Germany
| | - Christian Preußer
- a Institute of Biochemistry, Justus Liebig University of Giessen , D-35392 Giessen , Germany
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33
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Hutchinson S, Glover L, Horn D. High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes. BMC Genomics 2016; 17:806. [PMID: 27756224 PMCID: PMC5070307 DOI: 10.1186/s12864-016-3154-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/11/2016] [Indexed: 11/10/2022] Open
Abstract
Background African trypanosomes cause lethal diseases in humans and animals and escape host immune attack by switching the expression of Variant Surface Glycoprotein (VSG) genes. The expressed VSGs are located at the ends of telomeric, polycistronic transcription units known as VSG expression sites (VSG-ESs). Each cell has many VSG-ESs but only one is transcribed in bloodstream-form parasites and all of them are inactive upon transmission to the insect vector mid-gut; a subset of monocistronic metacyclic VSG-ESs are then activated in the insect salivary gland. Deep-sequence analyses have been informative but assigning sequences to individual VSG-ESs has been challenging because they each contain closely related expression-site associated genes, or ESAGs, thought to contribute to virulence. Results We utilised ART, an in silico short read simulator to demonstrate the feasibility of accurately aligning reads to VSG-ESs. Then, using high-resolution transcriptomes from isogenic bloodstream and insect-stage Lister 427 Trypanosoma brucei, we uncover increased abundance in the insect mid-gut stage of mRNAs from metacyclic VSG-ESs and of mRNAs from the unusual ESAG, ESAG10. Further, we show that the silencing associated with allelic exclusion involves repression focussed at the ends of the VSG-ESs. We also use the approach to report relative fitness costs following ESAG RNAi from a genome-scale screen. Conclusions By assigning sequences to individual VSG-ESs we provide new insights into VSG-ES transcription control, allelic exclusion and impacts on fitness. Thus, deeper insights into the expression and function of regulated multi-gene families are more accessible than previously anticipated. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3154-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian Hutchinson
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Lucy Glover
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.,Present address: Trypanosomes Molecular Biology, Institut Pasteur, 75015, Paris, France
| | - David Horn
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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Laffitte MCN, Leprohon P, Papadopoulou B, Ouellette M. Plasticity of the Leishmania genome leading to gene copy number variations and drug resistance. F1000Res 2016; 5:2350. [PMID: 27703673 PMCID: PMC5031125 DOI: 10.12688/f1000research.9218.1] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 01/04/2023] Open
Abstract
Leishmania has a plastic genome, and drug pressure can select for gene copy number variation (CNV). CNVs can apply either to whole chromosomes, leading to aneuploidy, or to specific genomic regions. For the latter, the amplification of chromosomal regions occurs at the level of homologous direct or inverted repeated sequences leading to extrachromosomal circular or linear amplified DNAs. This ability of
Leishmania to respond to drug pressure by CNVs has led to the development of genomic screens such as Cos-Seq, which has the potential of expediting the discovery of drug targets for novel promising drug candidates.
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Affiliation(s)
- Marie-Claude N Laffitte
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Barbara Papadopoulou
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU Québec, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
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35
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Antwi EB, Haanstra JR, Ramasamy G, Jensen B, Droll D, Rojas F, Minia I, Terrao M, Mercé C, Matthews K, Myler PJ, Parsons M, Clayton C. Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression. BMC Genomics 2016; 17:306. [PMID: 27118143 PMCID: PMC4845500 DOI: 10.1186/s12864-016-2624-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/16/2016] [Indexed: 11/25/2022] Open
Abstract
Background Trypanosoma brucei is a unicellular parasite which multiplies in mammals (bloodstream form) and Tsetse flies (procyclic form). Trypanosome RNA polymerase II transcription is polycistronic, individual mRNAs being excised by trans splicing and polyadenylation. We previously made detailed measurements of mRNA half-lives in bloodstream and procyclic forms, and developed a mathematical model of gene expression for bloodstream forms. At the whole transcriptome level, many bloodstream-form mRNAs were less abundant than was predicted by the model. Results We refined the published mathematical model and extended it to the procyclic form. We used the model, together with known mRNA half-lives, to predict the abundances of individual mRNAs, assuming rapid, unregulated mRNA processing; then we compared the results with measured mRNA abundances. Remarkably, the abundances of most mRNAs in procyclic forms are predicted quite well by the model, being largely explained by variations in mRNA decay rates and length. In bloodstream forms substantially more mRNAs are less abundant than predicted. We list mRNAs that are likely to show particularly slow or inefficient processing, either in both forms or with developmental regulation. We also measured ribosome occupancies of all mRNAs in trypanosomes grown in the same conditions as were used to measure mRNA turnover. In procyclic forms there was a weak positive correlation between ribosome density and mRNA half-life, suggesting cross-talk between translation and mRNA decay; ribosome density was related to the proportion of the mRNA on polysomes, indicating control of translation initiation. Ribosomal protein mRNAs in procyclics appeared to be exceptionally rapidly processed but poorly translated. Conclusions Levels of mRNAs in procyclic form trypanosomes are determined mainly by length and mRNA decay, with some control of precursor processing. In bloodstream forms variations in nuclear events play a larger role in transcriptome regulation, suggesting aquisition of new control mechanisms during adaptation to mammalian parasitism. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2624-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enoch B Antwi
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Jurgen R Haanstra
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.,Systems Bioinformatics, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Gowthaman Ramasamy
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Seattle, WA, 98109-5219, USA
| | - Bryan Jensen
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Seattle, WA, 98109-5219, USA
| | - Dorothea Droll
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany.,Current address: Biology of Host Parasite Interactions, 25 rue du Docteur Roux, 75724, Paris cedex 15, France
| | - Federico Rojas
- Centre for Immunity, Infection and Evolution, Institute for Immunology and infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Igor Minia
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Monica Terrao
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Clémentine Mercé
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Keith Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Peter J Myler
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Seattle, WA, 98109-5219, USA.,Department of Global Health, University of Washington, Harris Hydraulics Building, 1705 NE Pacific St #310E, Box 357965, Seattle, WA, 98195, USA.,Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98195, USA
| | - Marilyn Parsons
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Seattle, WA, 98109-5219, USA.,Department of Global Health, University of Washington, Harris Hydraulics Building, 1705 NE Pacific St #310E, Box 357965, Seattle, WA, 98195, USA
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany.
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36
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Base J and H3.V Regulate Transcriptional Termination in Trypanosoma brucei. PLoS Genet 2016; 12:e1005762. [PMID: 26796638 PMCID: PMC4721952 DOI: 10.1371/journal.pgen.1005762] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 12/02/2015] [Indexed: 11/25/2022] Open
Abstract
Trypanosoma brucei is a protozoan parasite that lacks many transcription factors found in other eukaryotes, such as those whose binding demarcates enhancers. T. brucei retains histone variants and modifications, however, and it is hypothesized that it relies on epigenetic marks to define transcription-related boundaries. The histone H3 variant (H3.V) and an alternate nucleotide, base J (ß-D-glucosyl-hydroxymethyluracil), are two chromatin marks found at both transcription termination sites (TTSs) and telomeres. Here, we report that the absence of both base J and H3.V result in transcription readthrough and the appearance of antisense transcripts near TTSs. Additionally, we find that maintaining the transcriptional silencing of pol I-transcribed telomeric Variant Surface Glycoprotein (VSG) genes appears to be dependent on deposition of H3.V alone. Our study reveals that gene expression depends on different epigenetic cues depending on chromosomal location and on the transcribing polymerase. This work provides insight into how these signals may have evolved into the more nuanced and fine-tuned gene regulatory mechanisms observed in other model systems. In eukaryotes, DNA is wrapped around histones to form chromatin. Modifications on the DNA itself, or on the canonical histones around which the DNA is wrapped, can lead to changes in gene expression. Alternate histones are also used to regulate gene expression. The African trypanosome, the causative agent of African sleeping sickness, transcribes its genes in long arrays called polycistronic transcription units (PTUs). In this study, we describe how the African Trypanosome uses two chromatin marks to regulate genes that lie close to the end of the PTU or close to the ends of chromosomes, called telomeres. One mark, base J, is on the DNA itself, while the other utilized mark is an alternate histone protein called H3.V. In the absence of these marks, there is an increase in antisense RNA that corresponds to genes that lie near the ends of the PTUs, and an increase in sense RNA for genes near telomeres. Since trypanosomes are evolutionarily distant from humans, these findings shed light on how gene expression mechanisms that are modulated by chromatin marks may have evolved to produce the complex gene regulatory networks found in our own tissues.
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De Gaudenzi JG, Jäger AV, Izcovich R, Campo VA. Insights into the Regulation of mRNA Processing of Polycistronic Transcripts Mediated by DRBD4/PTB2, a Trypanosome Homolog of the Polypyrimidine Tract-Binding Protein. J Eukaryot Microbiol 2016; 63:440-52. [PMID: 26663092 DOI: 10.1111/jeu.12288] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/11/2015] [Accepted: 12/02/2015] [Indexed: 12/13/2022]
Abstract
Trypanosomes regulate gene expression mostly by posttranscriptional mechanisms, including control of mRNA turnover and translation efficiency. This regulation is carried out via certain elements located at the 3'-untranslated regions of mRNAs, which are recognized by RNA-binding proteins. In trypanosomes, trans-splicing is of central importance to control mRNA maturation. We have previously shown that TcDRBD4/PTB2, a trypanosome homolog of the human polypyrimidine tract-binding protein splicing regulator, interacts with the intergenic region of one specific dicistronic transcript, referred to as TcUBP (and encoding for TcUBP1 and TcUBP2, two closely kinetoplastid-specific proteins). In this work, a survey of TcUBP RNA processing revealed certain TcDRBD4/PTB2-regulatory elements within its intercistronic region, which are likely to influence the trans-splicing rate of monocistronic-derived transcripts. Furthermore, TcDRBD4/PTB2 overexpression in epimastigote cells notably decreased both UBP1 and UBP2 protein expression. This type of posttranscriptional gene regulatory mechanism could be extended to other transcripts as well, as we identified several other RNA precursor molecules that specifically bind to TcDRBD4/PTB2. Altogether, these findings support a model in which TcDRBD4/PTB2-containing ribonucleoprotein complexes can prevent trans-splicing. This could represent another stage of gene expression regulation mediated by the masking of trans-splicing/polyadenylation signals.
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Affiliation(s)
- Javier G De Gaudenzi
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
| | - Adriana V Jäger
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
| | - Ronan Izcovich
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
| | - Vanina A Campo
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, UNSAM-CONICET, Sede San Martín, Prov. de Buenos Aires, Argentina
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Dillon LAL, Suresh R, Okrah K, Corrada Bravo H, Mosser DM, El-Sayed NM. Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions. BMC Genomics 2015; 16:1108. [PMID: 26715493 PMCID: PMC4696162 DOI: 10.1186/s12864-015-2237-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/24/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Parasites of the genus Leishmania are the causative agents of leishmaniasis, a group of diseases that range in manifestations from skin lesions to fatal visceral disease. The life cycle of Leishmania parasites is split between its insect vector and its mammalian host, where it resides primarily inside of macrophages. Once intracellular, Leishmania parasites must evade or deactivate the host's innate and adaptive immune responses in order to survive and replicate. RESULTS We performed transcriptome profiling using RNA-seq to simultaneously identify global changes in murine macrophage and L. major gene expression as the parasite entered and persisted within murine macrophages during the first 72 h of an infection. Differential gene expression, pathway, and gene ontology analyses enabled us to identify modulations in host and parasite responses during an infection. The most substantial and dynamic gene expression responses by both macrophage and parasite were observed during early infection. Murine genes related to both pro- and anti-inflammatory immune responses and glycolysis were substantially upregulated and genes related to lipid metabolism, biogenesis, and Fc gamma receptor-mediated phagocytosis were downregulated. Upregulated parasite genes included those aimed at mitigating the effects of an oxidative response by the host immune system while downregulated genes were related to translation, cell signaling, fatty acid biosynthesis, and flagellum structure. CONCLUSIONS The gene expression patterns identified in this work yield signatures that characterize multiple developmental stages of L. major parasites and the coordinated response of Leishmania-infected macrophages in the real-time setting of a dual biological system. This comprehensive dataset offers a clearer and more sensitive picture of the interplay between host and parasite during intracellular infection, providing additional insights into how pathogens are able to evade host defenses and modulate the biological functions of the cell in order to survive in the mammalian environment.
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Affiliation(s)
- Laura A L Dillon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA. .,Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Rahul Suresh
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
| | - Kwame Okrah
- Department of Mathematics, University of Maryland, College Park, MD, 20742, USA.
| | - Hector Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA. .,Department of Computer Science, University of Maryland, College Park, MD, 20742, USA.
| | - David M Mosser
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA. .,Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA. .,Present Address: 3128 Bioscience Research Bldg., University of Maryland, College Park, MD, 20742, USA.
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Dillon LAL, Okrah K, Hughitt VK, Suresh R, Li Y, Fernandes MC, Belew AT, Corrada Bravo H, Mosser DM, El-Sayed NM. Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation. Nucleic Acids Res 2015; 43:6799-813. [PMID: 26150419 PMCID: PMC4538839 DOI: 10.1093/nar/gkv656] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Protozoan parasites of the genus Leishmania are the etiological agents of leishmaniasis, a group of diseases with a worldwide incidence of 0.9–1.6 million cases per year. We used RNA-seq to conduct a high-resolution transcriptomic analysis of the global changes in gene expression and RNA processing events that occur as L. major transforms from non-infective procyclic promastigotes to infective metacyclic promastigotes. Careful statistical analysis across multiple biological replicates and the removal of batch effects provided a high quality framework for comprehensively analyzing differential gene expression and transcriptome remodeling in this pathogen as it acquires its infectivity. We also identified precise 5′ and 3′ UTR boundaries for a majority of Leishmania genes and detected widespread alternative trans-splicing and polyadenylation. An investigation of possible correlations between stage-specific preferential trans-splicing or polyadenylation sites and differentially expressed genes revealed a lack of systematic association, establishing that differences in expression levels cannot be attributed to stage-regulated alternative RNA processing. Our findings build on and improve existing expression datasets and provide a substantially more detailed view of L. major biology that will inform the field and potentially provide a stronger basis for drug discovery and vaccine development efforts.
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Affiliation(s)
- Laura A L Dillon
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Kwame Okrah
- Department of Mathematics, University of Maryland, College Park, MD 20742, USA
| | - V Keith Hughitt
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Rahul Suresh
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Yuan Li
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Maria Cecilia Fernandes
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - A Trey Belew
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Hector Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - David M Mosser
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
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Bühlmann M, Walrad P, Rico E, Ivens A, Capewell P, Naguleswaran A, Roditi I, Matthews KR. NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway. Nucleic Acids Res 2015; 43:4491-504. [PMID: 25873624 PMCID: PMC4482084 DOI: 10.1093/nar/gkv330] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 02/03/2023] Open
Abstract
Trypanosomes mostly regulate gene expression through post-transcriptional mechanisms, particularly mRNA stability. However, much mRNA degradation is cytoplasmic such that mRNA nuclear export must represent an important level of regulation. Ribosomal RNAs must also be exported from the nucleus and the trypanosome orthologue of NMD3 has been confirmed to be involved in rRNA processing and export, matching its function in other organisms. Surprisingly, we found that TbNMD3 depletion also generates mRNA accumulation of procyclin-associated genes (PAGs), these being co-transcribed by RNA polymerase I with the procyclin surface antigen genes expressed on trypanosome insect forms. By whole transcriptome RNA-seq analysis of TbNMD3-depleted cells we confirm the regulation of the PAG transcripts by TbNMD3 and using reporter constructs reveal that PAG1 regulation is mediated by its 5'UTR. Dissection of the mechanism of regulation demonstrates that it is not dependent upon translational inhibition mediated by TbNMD3 depletion nor enhanced transcription. However, depletion of the nuclear export factors XPO1 or MEX67 recapitulates the effects of TbNMD3 depletion on PAG mRNAs and mRNAs accumulated in the nucleus of TbNMD3-depleted cells. These results invoke a novel RNA regulatory mechanism involving the NMD3-dependent nuclear export of mRNA cargos, suggesting a shared platform for mRNA and rRNA export.
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Affiliation(s)
- Melanie Bühlmann
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Pegine Walrad
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK Centre for Immunology and Infection, Department of Biology, University of York, YO10 5DD, UK
| | - Eva Rico
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Alasdair Ivens
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | - Paul Capewell
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
| | | | - Isabel Roditi
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland
| | - Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Kings Buildings, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
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Matthews KR. 25 years of African trypanosome research: From description to molecular dissection and new drug discovery. Mol Biochem Parasitol 2015; 200:30-40. [PMID: 25736427 PMCID: PMC4509711 DOI: 10.1016/j.molbiopara.2015.01.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 01/27/2023]
Abstract
The Molecular Parasitology conference was first held at the Marine Biological laboratory, Woods Hole, USA 25 years ago. Since that first meeting, the conference has evolved and expanded but has remained the showcase for the latest research developments in molecular parasitology. In this perspective, I reflect on the scientific discoveries focussed on African trypanosomes (Trypanosoma brucei spp.) that have occurred since the inaugural MPM meeting and discuss the current and future status of research on these parasites.
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Affiliation(s)
- Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.
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Mandal G, Mandal S, Sharma M, Charret KS, Papadopoulou B, Bhattacharjee H, Mukhopadhyay R. Species-specific antimonial sensitivity in Leishmania is driven by post-transcriptional regulation of AQP1. PLoS Negl Trop Dis 2015; 9:e0003500. [PMID: 25714343 PMCID: PMC4340957 DOI: 10.1371/journal.pntd.0003500] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/28/2014] [Indexed: 11/26/2022] Open
Abstract
Leishmania is a digenetic protozoan parasite causing leishmaniasis in humans. The different clinical forms of leishmaniasis are caused by more than twenty species of Leishmania that are transmitted by nearly thirty species of phlebotomine sand flies. Pentavalent antimonials (such as Pentostam or Glucantime) are the first line drugs for treating leishmaniasis. Recent studies suggest that pentavalent antimony (Sb(V)) acts as a pro-drug, which is converted to the more active trivalent form (Sb(III)). However, sensitivity to trivalent antimony varies among different Leishmania species. In general, Leishmania species causing cutaneous leishmaniasis (CL) are more sensitive to Sb(III) than the species responsible for visceral leishmaniasis (VL). Leishmania aquaglyceroporin (AQP1) facilitates the adventitious passage of antimonite down a concentration gradient. In this study, we show that Leishmania species causing CL accumulate more antimonite, and therefore exhibit higher sensitivity to antimonials, than the species responsible for VL. This species-specific differential sensitivity to antimonite is directly proportional to the expression levels of AQP1 mRNA. We show that the stability of AQP1 mRNA in different Leishmania species is regulated by their respective 3’-untranslated regions. The differential regulation of AQP1 mRNA explains the distinct antimonial sensitivity of each species. The degree of response to antimonial drugs varies widely between species and even among strains of the same species of the protozoan parasite Leishmania. However, the molecular mechanism(s) is unknown. In this study, we show that Leishmania aquaglyceroporin AQP1 drives this species-specific antimonial resistance. Aquaglyceroporins are channel proteins that facilitate the passage of small uncharged molecules, such as glycerol and water, across the biological membranes. AQP1 helps the parasite cope with the osmotic challenges it faces during its life cycle. Additionally, AQP1 is an adventitious facilitator of antimonite, the active form of pentavalent antimonial drugs. We show that AQP1 expression level is species-specific, and less AQP1 in visceral species compared to the cutaneous species results in increased resistance to antimonials. We also demonstrate that the 3’-untranslated regions (3’-UTR) of the AQP1 mRNA is a major determining factor of species-specific regulation of AQP1. Along with water homeostasis, aquaglyceroporins are also involved in directed cell migration. The variable levels of AQP1 in different Leishmania species may enable them to find their appropriate niches in vertebrate hosts and cope with the species-specific osmotic challenges during their life cycles.
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Affiliation(s)
- Goutam Mandal
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Florida, United States of America
| | - Srotoswati Mandal
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Florida, United States of America
| | - Mansi Sharma
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Florida, United States of America
| | - Karen Santos Charret
- CHU de Quebec Research Center and Department of Microbiology-Infectious Disease and Immunology, University Laval, Quebec, Canada
| | - Barbara Papadopoulou
- CHU de Quebec Research Center and Department of Microbiology-Infectious Disease and Immunology, University Laval, Quebec, Canada
| | - Hiranmoy Bhattacharjee
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Florida, United States of America
| | - Rita Mukhopadhyay
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Florida, United States of America
- * E-mail:
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Bartholomeu DC, de Paiva RMC, Mendes TAO, DaRocha WD, Teixeira SMR. Unveiling the intracellular survival gene kit of trypanosomatid parasites. PLoS Pathog 2014; 10:e1004399. [PMID: 25474314 PMCID: PMC4256449 DOI: 10.1371/journal.ppat.1004399] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Trypanosomatids are unicellular protozoans of medical and economical relevance since they are the etiologic agents of infectious diseases in humans as well as livestock. Whereas Trypanosoma cruzi and different species of Leishmania are obligate intracellular parasites, Trypanosoma brucei and other trypanosomatids develop extracellularly throughout their entire life cycle. After their genomes have been sequenced, various comparative genomic studies aimed at identifying sequences involved with host cell invasion and intracellular survival have been described. However, for only a handful of genes, most of them present exclusively in the T. cruzi or Leishmania genomes, has there been any experimental evidence associating them with intracellular parasitism. With the increasing number of published complete genome sequences of members of the trypanosomatid family, including not only different Trypanosoma and Leishmania strains and subspecies but also trypanosomatids that do not infect humans or other mammals, we may now be able to contemplate a slightly better picture regarding the specific set of parasite factors that defines each organism's mode of living and the associated disease phenotypes. Here, we review the studies concerning T. cruzi and Leishmania genes that have been implicated with cell invasion and intracellular parasitism and also summarize the wealth of new information regarding the mode of living of intracellular parasites that is resulting from comparative genome studies that are based on increasingly larger trypanosomatid genome datasets.
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Affiliation(s)
| | - Rita Marcia Cardoso de Paiva
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago A. O. Mendes
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Wanderson D. DaRocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Parana, Brazil
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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Inoue AH, Serpeloni M, Hiraiwa PM, Yamada-Ogatta SF, Muniz JRC, Motta MCM, Vidal NM, Goldenberg S, Ávila AR. Identification of a novel nucleocytoplasmic shuttling RNA helicase of trypanosomes. PLoS One 2014; 9:e109521. [PMID: 25313564 PMCID: PMC4196910 DOI: 10.1371/journal.pone.0109521] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression in trypanosomes is controlled mostly by post-transcriptional pathways. Little is known about the components of mRNA nucleocytoplasmic export routes in these parasites. Comparative genomics has shown that the mRNA transport pathway is the least conserved pathway among eukaryotes. Nonetheless, we identified a RNA helicase (Hel45) that is conserved across eukaryotes and similar to shuttling proteins involved in mRNA export. We used in silico analysis to predict the structure of Trypanosoma cruzi Hel45, including the N-terminal domain and the C-terminal domain, and our findings suggest that this RNA helicase can form complexes with mRNA. Hel45 was present in both nucleus and cytoplasm. Electron microscopy showed that Hel45 is clustered close to the cytoplasmic side of nuclear pore complexes, and is also present in the nucleus where it is associated with peripheral compact chromatin. Deletion of a predicted Nuclear Export Signal motif led to the accumulation of Hel45ΔNES in the nucleus, indicating that Hel45 shuttles between the nucleus and the cytoplasm. This transport was dependent on active transcription but did not depend on the exportin Crm1. Knockdown of Mex67 in T. brucei caused the nuclear accumulation of the T. brucei ortholog of Hel45. Indeed, Hel45 is present in mRNA ribonucleoprotein complexes that are not associated with polysomes. It is still necessary to confirm the precise function of Hel45. However, this RNA helicase is associated with mRNA metabolism and its nucleocytoplasmic shuttling is dependent on an mRNA export route involving Mex67 receptor.
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Affiliation(s)
| | - Mariana Serpeloni
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- Departamento de Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | | | - Maria Cristina Machado Motta
- Departamento de Biologia Celular e Parasitologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Newton Medeiros Vidal
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Brazil
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Vieira HGS, Grynberg P, Bitar M, Pires SDF, Hilário HO, Macedo AM, Machado CR, de Andrade HM, Franco GR. Proteomic analysis of Trypanosoma cruzi response to ionizing radiation stress. PLoS One 2014; 9:e97526. [PMID: 24842666 PMCID: PMC4026238 DOI: 10.1371/journal.pone.0097526] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 04/22/2014] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, is extremely resistant to ionizing radiation, enduring up to 1.5 kGy of gamma rays. Ionizing radiation can damage the DNA molecule both directly, resulting in double-strand breaks, and indirectly, as a consequence of reactive oxygen species production. After a dose of 500 Gy of gamma rays, the parasite genome is fragmented, but the chromosomal bands are restored within 48 hours. Under such conditions, cell growth arrests for up to 120 hours and the parasites resume normal growth after this period. To better understand the parasite response to ionizing radiation, we analyzed the proteome of irradiated (4, 24, and 96 hours after irradiation) and non-irradiated T. cruzi using two-dimensional differential gel electrophoresis followed by mass spectrometry for protein identification. A total of 543 spots were found to be differentially expressed, from which 215 were identified. These identified protein spots represent different isoforms of only 53 proteins. We observed a tendency for overexpression of proteins with molecular weights below predicted, indicating that these may be processed, yielding shorter polypeptides. The presence of shorter protein isoforms after irradiation suggests the occurrence of post-translational modifications and/or processing in response to gamma radiation stress. Our results also indicate that active translation is essential for the recovery of parasites from ionizing radiation damage. This study therefore reveals the peculiar response of T. cruzi to ionizing radiation, raising questions about how this organism can change its protein expression to survive such a harmful stress.
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Affiliation(s)
| | - Priscila Grynberg
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
| | - Mainá Bitar
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Simone da Fonseca Pires
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Heron Oliveira Hilário
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andrea Mara Macedo
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Hélida Monteiro de Andrade
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glória Regina Franco
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Trypanosoma brucei translation initiation factor homolog EIF4E6 forms a tripartite cytosolic complex with EIF4G5 and a capping enzyme homolog. EUKARYOTIC CELL 2014; 13:896-908. [PMID: 24839125 DOI: 10.1128/ec.00071-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Trypanosomes lack the transcriptional control characteristic of the majority of eukaryotes that is mediated by gene-specific promoters in a one-gene-one-promoter arrangement. Rather, their genomes are transcribed in large polycistrons with no obvious functional linkage. Posttranscriptional regulation of gene expression must thus play a larger role in these organisms. The eIF4E homolog TbEIF4E6 binds mRNA cap analogs in vitro and is part of a complex in vivo that may fulfill such a role. Knockdown of TbEIF4E6 tagged with protein A-tobacco etch virus protease cleavage site-protein C to approximately 15% of the normal expression level resulted in viable cells that displayed a set of phenotypes linked to detachment of the flagellum from the length of the cell body, if not outright flagellum loss. While these cells appeared and behaved as normal under stationary liquid culture conditions, standard centrifugation resulted in a marked increase in flagellar detachment. Furthermore, the ability of TbEIF4E6-depleted cells to engage in social motility was reduced. The TbEIF4E6 protein forms a cytosolic complex containing a triad of proteins, including the eIF4G homolog TbEIF4G5 and a hypothetical protein of 70.3 kDa, referred to as TbG5-IP. The TbG5-IP analysis revealed two domains with predicted secondary structures conserved in mRNA capping enzymes: nucleoside triphosphate hydrolase and guanylyltransferase. These complex members have the potential for RNA interaction, either via the 5' cap structure for TbEIF4E6 and TbG5-IP or through RNA-binding domains in TbEIF4G5. The associated proteins provide a signpost for future studies to determine how this complex affects capped RNA molecules.
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Gupta SK, Chikne V, Eliaz D, Tkacz ID, Naboishchikov I, Carmi S, Waldman Ben-Asher H, Michaeli S. Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in Trypanosoma brucei. RNA Biol 2014; 11:715-31. [PMID: 24922194 DOI: 10.4161/rna.29143] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In trypanosomes, mRNAs are processed by trans-splicing; in this process, a common exon, the spliced leader, is added to all mRNAs from a small RNA donor, the spliced leader RNA (SL RNA). However, little is known regarding how this process is regulated. In this study we investigated the function of two serine-arginine-rich proteins, TSR1 and TSR1IP, implicated in trans-splicing in Trypanosoma brucei. Depletion of these factors by RNAi suggested their role in both cis- and trans-splicing. Microarray was used to examine the transcriptome of the silenced cells. The level of hundreds of mRNAs was changed, suggesting that these proteins have a role in regulating only a subset of T. brucei mRNAs. Mass-spectrometry analyses of complexes associated with these proteins suggest that these factors function in mRNA stability, translation, and rRNA processing. We further demonstrate changes in the stability of mRNA as a result of depletion of the two TSR proteins. In addition, rRNA defects were observed under the depletion of U2AF35, TSR1, and TSR1IP, but not SF1, suggesting involvement of SR proteins in rRNA processing.
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Affiliation(s)
- Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Vaibhav Chikne
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Dror Eliaz
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Itai Dov Tkacz
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Ilana Naboishchikov
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Shai Carmi
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, Israel
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Panunzi LG, Agüero F. A genome-wide analysis of genetic diversity in Trypanosoma cruzi intergenic regions. PLoS Negl Trop Dis 2014; 8:e2839. [PMID: 24784238 PMCID: PMC4006747 DOI: 10.1371/journal.pntd.0002839] [Citation(s) in RCA: 7] [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: 09/05/2013] [Accepted: 03/20/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi is the causal agent of Chagas Disease. Recently, the genomes of representative strains from two major evolutionary lineages were sequenced, allowing the construction of a detailed genetic diversity map for this important parasite. However this map is focused on coding regions of the genome, leaving a vast space of regulatory regions uncharacterized in terms of their evolutionary conservation and/or divergence. METHODOLOGY Using data from the hybrid CL Brener and Sylvio X10 genomes (from the TcVI and TcI Discrete Typing Units, respectively), we identified intergenic regions that share a common evolutionary ancestry, and are present in both CL Brener haplotypes (TcII-like and TcIII-like) and in the TcI genome; as well as intergenic regions that were conserved in only two of the three genomes/haplotypes analyzed. The genetic diversity in these regions was characterized in terms of the accumulation of indels and nucleotide changes. PRINCIPAL FINDINGS Based on this analysis we have identified i) a core of highly conserved intergenic regions, which remained essentially unchanged in independently evolving lineages; ii) intergenic regions that show high diversity in spite of still retaining their corresponding upstream and downstream coding sequences; iii) a number of defined sequence motifs that are shared by a number of unrelated intergenic regions. A fraction of indels explains the diversification of some intergenic regions by the expansion/contraction of microsatellite-like repeats.
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Affiliation(s)
- Leonardo G. Panunzi
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
- * E-mail: ;
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Miranda A, Samudio F, Saldaña A, Castillo J, Brandão A, Calzada JE. The calmodulin intergenic spacer as molecular target for characterization of Leishmania species. Parasit Vectors 2014; 7:35. [PMID: 24438764 PMCID: PMC4021611 DOI: 10.1186/1756-3305-7-35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/14/2014] [Indexed: 11/18/2022] Open
Abstract
Background Human leishmaniasis is a neglected disease caused by parasites of the genus Leishmania. Clinical aspects of this disease can vary significantly, reflecting the wide range of parasites in the genus Leishmania. Knowing accurately the Leishmania species infecting humans is important for clinical case management and evaluation of epidemiological risk. Calmodulin is an essential gene in trypanosomatids that modulates the calcium metabolism in various cellular activities. Despite its strong conservation in trypanosomatids, it has been recently observed that its untranslated regions (UTR) diverge among species. Methods In this study we analyzed the sequences and the absolute dinucleotide frequency of the intergenic spacer of the calmodulin gene (containing both, 3′ and 5′UTR) in nine reference Leishmania species and ten clinical isolates obtained from patients with cutaneous leishmaniasis. Results We show that the short calmodulin intergenic spacers exhibit features that make them interesting for applications in molecular characterization and phylogenetic studies of Leishmania. Dendrograms based on sequence alignments and on the dinucleotide frequency indicate that this particular region of calmodulin gene might be useful for species typing between the Leishmania and Viannia subgenera. Conclusions Mutations and composition of the calmodulin intergenic spacer from Leishmania species might have taxonomic value as parameters to define if an isolate is identical to a certain species or belongs to one of the two current subgenera.
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Affiliation(s)
| | | | | | | | | | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de Salud, Ciudad de Panamá, Panamá.
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Vasquez JJ, Hon CC, Vanselow JT, Schlosser A, Siegel TN. Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages. Nucleic Acids Res 2014; 42:3623-37. [PMID: 24442674 PMCID: PMC3973304 DOI: 10.1093/nar/gkt1386] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
While gene expression is a fundamental and tightly controlled cellular process that is regulated at multiple steps, the exact contribution of each step remains unknown in any organism. The absence of transcription initiation regulation for RNA polymerase II in the protozoan parasite Trypanosoma brucei greatly simplifies the task of elucidating the contribution of translation to global gene expression. Therefore, we have sequenced ribosome-protected mRNA fragments in T. brucei, permitting the genome-wide analysis of RNA translation and translational efficiency. We find that the latter varies greatly between life cycle stages of the parasite and ∼100-fold between genes, thus contributing to gene expression to a similar extent as RNA stability. The ability to map ribosome positions at sub-codon resolution revealed extensive translation from upstream open reading frames located within 5' UTRs and enabled the identification of hundreds of previously un-annotated putative coding sequences (CDSs). Evaluation of existing proteomics and genome-wide RNAi data confirmed the translation of previously un-annotated CDSs and suggested an important role for >200 of those CDSs in parasite survival, especially in the form that is infective to mammals. Overall our data show that translational control plays a prevalent and important role in different parasite life cycle stages of T. brucei.
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Affiliation(s)
- Juan-José Vasquez
- Research Center for Infectious Diseases, University of Wuerzburg, Wuerzburg 97080, Germany, Département Biologie cellulaire et infection, Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris 75015, France, INSERM U786, Paris 75015, France and Rudolf Virchow Center, University of Wuerzburg, Wuerzburg 97080, Germany
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