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Glutamine increases stability of TPH1 mRNA via p38 mitogen-activated kinase in mouse mastocytoma cells. Mol Biol Rep 2023; 50:267-277. [PMID: 36331742 PMCID: PMC9884262 DOI: 10.1007/s11033-022-07693-7] [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: 03/20/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
Expression changes for tryptophan hydroxylase 1 (TPH1), the rate-limiting enzyme in serotonin synthesis, by environmental glutamine (GLN) were examined in mouse mastocytoma-derived P815-HTR cells. GLN-treated cells exhibited a robust increase in TPH1 mRNA after a 6 h exposure to GLN. 6-Diazo-5-oxo-L-norleucine (DON), a glutamine-utilizing glutaminase inhibitor, significantly inhibited the GLN-induction of TPH1 mRNA. Nuclear run-on assays and mRNA decay experiments demonstrated that the primary mechanism leading to increased TPH1 mRNA levels was not due to transcriptional changes, but rather due to increased TPH1 RNA stability induced by GLN. Treatment with GLN also led to activation of p38 MAP kinase, but not p42/44 MAPK. In addition, SB203580, a p38 MAP kinase specific inhibitor, completely abolished the GLN-mediated increase of TPH1 mRNA levels, suggesting the pathway stabilizing TPH1 mRNA might be mediated by the activated p38 MAP kinase pathway. Additionally, SB203580 significantly reduced the stability of TPH1 mRNA, and this reduction of the stability was not affected by GLN in the culture medium, implying a sequential signaling from GLN being mediated by p38 MAP kinase, resulting in alteration of TPH1 mRNA stability. TPH1 mRNA stability loss was also dependent on de novo protein synthesis as shown by treatment of cells with a transcriptional/translational blocker. We provide evidence that TPH1 mRNA levels are increased in response to increased exogenous GLN in mouse mastocytoma cells via a stabilization of TPH1 mRNA due to the activity of the p38 MAP kinase.
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In Leishmania major, the Homolog of the Oncogene PES1 May Play a Critical Role in Parasite Infectivity. Int J Mol Sci 2021; 22:ijms222212592. [PMID: 34830469 PMCID: PMC8618447 DOI: 10.3390/ijms222212592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 01/09/2023] Open
Abstract
Leishmaniasis is a neglected tropical disease caused by Leishmania spp. The improvement of existing treatments and the discovery of new drugs remain ones of the major goals in control and eradication of this disease. From the parasite genome, we have identified the homologue of the human oncogene PES1 in Leishmania major (LmjPES). It has been demonstrated that PES1 is involved in several processes such as ribosome biogenesis, cell proliferation and genetic transcription. Our phylogenetic studies showed that LmjPES encodes a highly conserved protein containing three main domains: PES N-terminus (shared with proteins involved in ribosomal biogenesis), BRCT (found in proteins related to DNA repair processes) and MAEBL-type domain (C-terminus, related to erythrocyte invasion in apicomplexan). This gene showed its highest expression level in metacyclic promastigotes, the infective forms; by fluorescence microscopy assay, we demonstrated the nuclear localization of LmjPES protein. After generating mutant parasites overexpressing LmjPES, we observed that these clones displayed a dramatic increase in the ratio of cell infection within macrophages. Furthermore, BALB/c mice infected with these transgenic parasites exhibited higher footpad inflammation compared to those inoculated with non-overexpressing parasites.
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Roscoe S, Manni E, Roberts M, Ananvoranich S. Formation of mRNP granules in Toxoplasma gondii during the lytic cycle. Mol Biochem Parasitol 2020; 242:111349. [PMID: 33383066 DOI: 10.1016/j.molbiopara.2020.111349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/01/2022]
Abstract
Two poly(A) binding proteins (PABPs) of Toxoplasma gondii, were identified and characterized. They were named TgPABPC and TgPABPN as they were found to localize in the cytoplasm and nucleus respectively. TgPABPC, which colocalizes with mRNA granules, is therefore used as a cellular marker of mRNP granules. We detected that the formation of mRNP granules was independent of polymerized microtubules, and that the granules were distributed stochastically within the cytosol. Formation of mRNP granules was found to occur prior to parasite egress when a Ca2+ ionophore is used to induce egress. It was also found that maturation of mRNP granules could be described as a two-phase process. First, prior to host cell lysis, mRNP granules were formed rapidly within the cytosol. Second, the mRNP granule load was reduced within 10 min post egress. To investigate the link between translational state and mRNP granule formation, treatments with salubrinal, nutrient deprivation, and pH stress were used. While salubrinal induced granule formation in tachyzoites, nutrient starvation and pH stress showed no induction effect on mRNP granule formation. Interestingly, salubrinal treatment in bradyzoites did not induce RNP granule formation, thus suggesting that mRNP granule formation is not a ubiquitous response or directly related to translational repression. Instead, mRNP granule formation is likely a response to the rapid increase in non-translating RNA brought on by sudden changes in translational state.
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Affiliation(s)
- Scott Roscoe
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B3P4, Canada
| | - Emad Manni
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B3P4, Canada
| | - Mikayla Roberts
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B3P4, Canada
| | - Sirinart Ananvoranich
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B3P4, Canada.
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4
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Romagnoli BAA, Holetz FB, Alves LR, Goldenberg S. RNA Binding Proteins and Gene Expression Regulation in Trypanosoma cruzi. Front Cell Infect Microbiol 2020; 10:56. [PMID: 32154189 PMCID: PMC7045066 DOI: 10.3389/fcimb.2020.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/03/2020] [Indexed: 01/24/2023] Open
Abstract
The regulation of gene expression in trypanosomatids occurs mainly at the post-transcriptional level. In the case of Trypanosoma cruzi, the characterization of messenger ribonucleoprotein (mRNP) particles has allowed the identification of several classes of RNA binding proteins (RBPs), as well as non-canonical RBPs, associated with mRNA molecules. The protein composition of the mRNPs as well as the localization and functionality of the mRNAs depend on their associated proteins. mRNPs can also be organized into larger complexes forming RNA granules, which function as stress granules or P-bodies depending on the associated proteins. The fate of mRNAs in the cell, and consequently the genes expressed, depends on the set of proteins associated with the messenger molecule. These proteins allow the coordinated expression of mRNAs encoding proteins that are related in function, resulting in the formation of post-transcriptional operons. However, the puzzle posed by the combinatorial association of sets of RBPs with mRNAs and how this relates to the expressed genes remain to be elucidated. One important tool in this endeavor is the use of the CRISPR/CAS system to delete genes encoding RBPs, allowing the evaluation of their effect on the formation of mRNP complexes and associated mRNAs in the different compartments of the translation machinery. Accordingly, we recently established this methodology for T. cruzi and deleted the genes encoding RBPs containing zinc finger domains. In this manuscript, we will discuss the data obtained and the potential of the CRISPR/CAS methodology to unveil the role of RBPs in T. cruzi gene expression regulation.
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Affiliation(s)
- Bruno A A Romagnoli
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Fabiola B Holetz
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Lysangela R Alves
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
| | - Samuel Goldenberg
- Gene Expression Regulation Laboratory, Institute Carlos Chagas, Curitiba, Brazil
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Martínez-Calvillo S, Florencio-Martínez LE, Nepomuceno-Mejía T. Nucleolar Structure and Function in Trypanosomatid Protozoa. Cells 2019; 8:cells8050421. [PMID: 31071985 PMCID: PMC6562600 DOI: 10.3390/cells8050421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022] Open
Abstract
The nucleolus is the conspicuous nuclear body where ribosomal RNA genes are transcribed by RNA polymerase I, pre-ribosomal RNA is processed, and ribosomal subunits are assembled. Other important functions have been attributed to the nucleolus over the years. Here we review the current knowledge about the structure and function of the nucleolus in the trypanosomatid parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania ssp., which represent one of the earliest branching lineages among the eukaryotes. These protozoan parasites present a single nucleolus that is preserved throughout the closed nuclear division, and that seems to lack fibrillar centers. Trypanosomatids possess a relatively low number of rRNA genes, which encode rRNA molecules that contain large expansion segments, including several that are trypanosomatid-specific. Notably, the large subunit rRNA (28S-type) is fragmented into two large and four small rRNA species. Hence, compared to other organisms, the rRNA primary transcript requires additional processing steps in trypanosomatids. Accordingly, this group of parasites contains the highest number ever reported of snoRNAs that participate in rRNA processing. The number of modified rRNA nucleotides in trypanosomatids is also higher than in other organisms. Regarding the structure and biogenesis of the ribosomes, recent cryo-electron microscopy analyses have revealed several trypanosomatid-specific features that are discussed here. Additional functions of the nucleolus in trypanosomatids are also reviewed.
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Affiliation(s)
- Santiago Martínez-Calvillo
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Luis E Florencio-Martínez
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
| | - Tomás Nepomuceno-Mejía
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla CP 54090, Estado de México, Mexico.
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Wippel HH, Malgarin JS, Martins SDT, Vidal NM, Marcon BH, Miot HT, Marchini FK, Goldenberg S, Alves LR. The Nuclear RNA-binding Protein RBSR1 Interactome in Trypanosoma cruzi. J Eukaryot Microbiol 2018; 66:244-253. [PMID: 29984450 DOI: 10.1111/jeu.12666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/18/2022]
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, has been widely studied, reflecting both its medical importance and the particular features that make this pathogen an attractive model for basic biological studies. The repression of transcripts by messenger ribonucleoprotein (mRNP) complexes is an important pathway of post-transcriptional regulation in eukaryotes, including T. cruzi. RBSR1 is a serine-arginine (SR)-rich RNA-binding protein (RBP) in T. cruzi that contains one RNA-recognition motif (RRM); this protein has a primarily nuclear localization and is developmentally regulated, not being detected in metacyclic trypomastigotes. RBSR1 interacts with other RBPs, such as UBP1 and UBP2, and the nuclear SR-protein TRRM1. Phylogenetic analysis indicated that RBSR1 is orthologous to the human splicing factor SRSF7, what might indicate its possible involvement in pre-RNA processing. Accordingly, ribonomics data showed the enrichment of snoRNAs and snRNAs in the RBSR1 immunoprecipiatation complex, hence reinforcing the supposition that this protein might be involved in RNA processing in the nucleus.
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Affiliation(s)
- Helisa H Wippel
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Juliane S Malgarin
- Molecular Biology Institute of Paraná, IBMP, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Sharon de Toledo Martins
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Newton M Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland, 20894
| | - Bruna H Marcon
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Hálisson T Miot
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Fabricio K Marchini
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Samuel Goldenberg
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
| | - Lysangela R Alves
- Carlos Chagas Institute, FIOCRUZ, Rua Professor Algacyr Munhoz Mader 3775, Curitiba, Paraná, Brazil
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7
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Caeiro LD, Alba-Soto CD, Rizzi M, Solana ME, Rodriguez G, Chidichimo AM, Rodriguez ME, Sánchez DO, Levy GV, Tekiel V. The protein family TcTASV-C is a novel Trypanosoma cruzi virulence factor secreted in extracellular vesicles by trypomastigotes and highly expressed in bloodstream forms. PLoS Negl Trop Dis 2018; 12:e0006475. [PMID: 29727453 PMCID: PMC5955593 DOI: 10.1371/journal.pntd.0006475] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 05/16/2018] [Accepted: 04/24/2018] [Indexed: 12/19/2022] Open
Abstract
TcTASV-C is a protein family of about 15 members that is expressed only in the trypomastigote stage of Trypanosoma cruzi. We have previously shown that TcTASV-C is located at the parasite surface and secreted to the medium. Here we report that the expression of different TcTASV-C genes occurs simultaneously at the trypomastigote stage and while some secreted and parasite-associated products are found in both fractions, others are different. Secreted TcTASV-C are mainly shedded through trypomastigote extracellular vesicles, of which they are an abundant constituent, despite its scarce expression on culture-derived trypomastigotes. In contrast, TcTASV-C is highly expressed in bloodstream trypomastigotes; its upregulation in bloodstream parasites was observed in different T. cruzi strains and was specific for TcTASV-C, suggesting that some host-molecules trigger TcTASV-C expression. TcTASV-C is also strongly secreted by bloodstream parasites. A DNA prime—protein boost immunization scheme with TcTASV-C was only partially effective to control the infection in mice challenged with a highly virulent T. cruzi strain. Vaccination triggered a strong humoral response that delayed the appearance of bloodstream trypomastigotes at the early phase of the infection. Linear epitopes recognized by vaccinated mice were mapped within the TcTASV-C family motif, suggesting that blockade of secreted TcTASV-C impacts on the settlement of infection. Furthermore, although experimental and naturally T. cruzi-infected hosts did not react with antigens from extracellular vesicles, vaccinated and challenged mice recognized not only TcTASV-C but also other vesicle-antigens. We hypothesize that TcTASV-C is involved in the establishment of the initial T. cruzi infection in the mammalian host. Altogether, these results point towards TcTASV-C as a novel secreted virulence factor of T. cruzi trypomastigotes. Trypanosoma cruzi is the kinetoplastid parasite that causes Chagas’ disease, a neglected infection endemic in Latin America and emerging worldwide. Being vaccines currently unavailable and treatments not completely effective, identification and characterization of parasite molecules that can be target for these interventions are urgently needed. Of particular interest are surface anchored and secreted proteins involved in parasite—host interplay. Recently, extracellular vesicles released from protozoan pathogens have been shown to alter host cell function favoring the establishment of infection. Trypomastigotes are the disseminating stage of T. cruzi, being their presence in peripheral blood a hallmark of early acute infection in mammals. While the most abundant proteins of the trypomastigote surface are fairly well characterized, little is known about other, less abundant and more recently discovered multigenic families, which could have critical functions in the parasite—host interaction. The T. cruziTrypomastigote Alanine, Valine and Serine rich proteins (TcTASV) belong to a medium-size multigene family of ~40 members that remained unobserved until a few years ago when it was identified through a trypomastigote-enriched cDNA library. Almost simultaneously, an expression library immunization approach designed to discover novel vaccine antigens in T. cruzi, spotlighted the TcTASV-C subfamily, as a fragment of a TcTASV-C gene was identified in a pool of protective clones. A distinctive feature that characterizes TcTASV proteins–and particularly the TcTASV-C subfamily- is their predominant expression in trypomastigotes. Recent transcriptomic and proteomic studies uphold our previous observations that the TcTASV family is over-represented in the trypomastigote stage, and therefore could represent an interesting target for rational intervention against T. cruzi infection. Here show that TcTASV-C is mainly secreted through extracellular vesicles (EVs) of trypomastigotes, and is a major cargo of its content. We have also shown that TcTASV-C is much more expressed in trypomastigotes purified from blood from infected mice than in trypomastigotes harvested from in vitro cultures, suggesting that host molecules should trigger TcTASV-C expression in vivo during the infection. The immunization of mice with TcTASV-C interfered with the early acute phase of T. cruzi infection through a strong humoral immune response. TcTASV-C should be considered as a novel secreted virulence factor of T. cruzi trypomastigotes and -although its biological function is still unknown- we hypothesize its participation in the early steps of T cruzi infection in the mammalian host.
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Affiliation(s)
- Lucas D Caeiro
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Catalina D Alba-Soto
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), UBA-CONICET, Buenos Aires, Argentina
| | - Mariana Rizzi
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - María Elisa Solana
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), UBA-CONICET, Buenos Aires, Argentina.,Departamento de Cs. Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
| | - Giselle Rodriguez
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Agustina M Chidichimo
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Matías E Rodriguez
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Daniel O Sánchez
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Gabriela V Levy
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
| | - Valeria Tekiel
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
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8
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Sabale PM, Ambi UB, Srivatsan SG. A Lucifer-Based Environment-Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs. Chembiochem 2018; 19:826-835. [PMID: 29396904 PMCID: PMC5972818 DOI: 10.1002/cbic.201700661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore (1,8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them.
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Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
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9
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Oliveira C, Faoro H, Alves LR, Goldenberg S. RNA-binding proteins and their role in the regulation of gene expression in Trypanosoma cruzi and Saccharomyces cerevisiae. Genet Mol Biol 2017; 40:22-30. [PMID: 28463381 PMCID: PMC5409782 DOI: 10.1590/1678-4685-gmb-2016-0258] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) have important functions in the regulation of gene
expression. RBPs play key roles in post-transcriptional processes in all eukaryotes,
such as splicing regulation, mRNA transport and modulation of mRNA translation and
decay. RBPs assemble into different mRNA-protein complexes, which form messenger
ribonucleoprotein complexes (mRNPs). Gene expression regulation in trypanosomatids
occurs mainly at the post-transcriptional level and RBPs play a key role in all
processes. However, the functional characterization of RBPs in Trypanosoma
cruzi has been impaired due to the lack of reliable reverse genetic
manipulation tools. The comparison of RBPs from Saccharomyces
cerevisiae and T. cruzi might allow inferring on the
function of these proteins based on the information available for the orthologous
RNA-binding proteins from the S. cerevisiae model organism. In this
review, we discuss the role of some RBPs from T. cruzi and their
homologues in regulating gene expression in yeast.
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Affiliation(s)
- Camila Oliveira
- Instituto Carlos Chagas, Fiocruz-Paraná, Curitiba, PR, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas, Fiocruz-Paraná, Curitiba, PR, Brazil
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Pastro L, Smircich P, Di Paolo A, Becco L, Duhagon MA, Sotelo-Silveira J, Garat B. Nuclear Compartmentalization Contributes to Stage-Specific Gene Expression Control in Trypanosoma cruzi. Front Cell Dev Biol 2017; 5:8. [PMID: 28243589 PMCID: PMC5303743 DOI: 10.3389/fcell.2017.00008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/25/2017] [Indexed: 12/24/2022] Open
Abstract
In the protozoan parasite Trypanosoma cruzi, as in other trypanosomatids, transcription of protein coding genes occurs in a constitutive fashion, producing large polycistronic transcription units. These units are composed of non-functionally related genes which are pervasively processed to yield each mRNA. Therefore, post-transcriptional processes are crucial to regulate gene expression. Considering that nuclear compartmentalization could contribute to gene expression regulation, we comparatively studied the nuclear, cytoplasmic and whole cell transcriptomes of the non-infective epimastigote stage of T. cruzi, using RNA-Seq. We found that the cytoplasmic transcriptome tightly correlates with the whole cell transcriptome and both equally correlate with the proteome. Nonetheless, 1,200 transcripts showed differential abundance between the nuclear and cytoplasmic fractions. For the genes with transcript content augmented in the nucleus, significant structural and compositional differences were found. The analysis of the reported epimastigote translatome and proteome, revealed scarce ribosome footprints and encoded proteins for them. Ontology analyses unveiled that many of these genes are distinctive of other parasite life-cycle stages. Finally, the relocalization of transcript abundance in the metacyclic trypomastigote infective stage was confirmed for specific genes. While gene expression is strongly dependent on transcript steady-state level, we here highlight the importance of the distribution of transcripts abundance between compartments in T. cruzi. Particularly, we show that nuclear compartmentation is playing an active role in the developmental stage determination preventing off-stage expression.
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Affiliation(s)
- Lucía Pastro
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la RepúblicaMontevideo, Uruguay; Departamento de Genética, Facultad de Medicina, Universidad de la RepúblicaMontevideo, Uruguay
| | - Pablo Smircich
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la RepúblicaMontevideo, Uruguay; Departamento de Genética, Facultad de Medicina, Universidad de la RepúblicaMontevideo, Uruguay
| | - Andrés Di Paolo
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable Montevideo, Uruguay
| | - Lorena Becco
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - María A Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la RepúblicaMontevideo, Uruguay; Departamento de Genética, Facultad de Medicina, Universidad de la RepúblicaMontevideo, Uruguay
| | - José Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable Montevideo, Uruguay
| | - Beatriz Garat
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
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11
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Hope R, Egarmina K, Voloshin K, Waldman Ben-Asher H, Carmi S, Eliaz D, Drori Y, Michaeli S. Transcriptome and proteome analyses and the role of atypical calpain protein and autophagy in the spliced leader silencing pathway in Trypanosoma brucei. Mol Microbiol 2016; 102:1-21. [PMID: 27161313 DOI: 10.1111/mmi.13417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2016] [Indexed: 11/29/2022]
Abstract
Under persistent ER stress, Trypanosoma brucei parasites induce the spliced leader silencing (SLS) pathway. In SLS, transcription of the SL RNA gene, the SL donor to all mRNAs, is extinguished, arresting trans-splicing and leading to programmed cell death (PCD). In this study, we investigated the transcriptome following silencing of SEC63, a factor essential for protein translocation across the ER membrane, and whose silencing induces SLS. The proteome of SEC63-silenced cells was analyzed with an emphasis on SLS-specific alterations in protein expression, and modifications that do not directly result from perturbations in trans-splicing. One such protein identified is an atypical calpain SKCRP7.1/7.2. Co-silencing of SKCRP7.1/7.2 and SEC63 eliminated SLS induction due its role in translocating the PK3 kinase. This kinase initiates SLS by migrating to the nucleus and phosphorylating TRF4 leading to shut-off of SL RNA transcription. Thus, SKCRP7.1 is involved in SLS signaling and the accompanying PCD. The role of autophagy in SLS was also investigated; eliminating autophagy through VPS34 or ATG7 silencing demonstrated that autophagy is not essential for SLS induction, but is associated with PCD. Thus, this study identified factors that are used by the parasite to cope with ER stress and to induce SLS and PCD.
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Affiliation(s)
- Ronen Hope
- The Mina and Everard Goodman Faculty of Life Sciences.,Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Katarina Egarmina
- The Mina and Everard Goodman Faculty of Life Sciences.,Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Konstantin Voloshin
- The Mina and Everard Goodman Faculty of Life Sciences.,Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | | | - Shai Carmi
- The Mina and Everard Goodman Faculty of Life Sciences.,Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Dror Eliaz
- The Mina and Everard Goodman Faculty of Life Sciences.,Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yaron Drori
- The Mina and Everard Goodman Faculty of Life Sciences.,Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences. .,Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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12
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Alves LR, Goldenberg S. RNA-binding proteins related to stress response and differentiation in protozoa. World J Biol Chem 2016; 7:78-87. [PMID: 26981197 PMCID: PMC4768126 DOI: 10.4331/wjbc.v7.i1.78] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 09/23/2015] [Accepted: 11/17/2015] [Indexed: 02/05/2023] Open
Abstract
RNA-binding proteins (RBPs) are key regulators of gene expression. There are several distinct families of RBPs and they are involved in the cellular response to environmental changes, cell differentiation and cell death. The RBPs can differentially combine with RNA molecules and form ribonucleoprotein (RNP) complexes, defining the function and fate of RNA molecules in the cell. RBPs display diverse domains that allow them to be categorized into distinct families. They play important roles in the cellular response to physiological stress, in cell differentiation, and, it is believed, in the cellular localization of certain mRNAs. In several protozoa, a physiological stress (nutritional, temperature or pH) triggers differentiation to a distinct developmental stage. Most of the RBPs characterized in protozoa arise from trypanosomatids. In these protozoa gene expression regulation is mostly post-transcriptional, which suggests that some RBPs might display regulatory functions distinct from those described for other eukaryotes. mRNA stability can be altered as a response to stress. Transcripts are sequestered to RNA granules that ultimately modulate their availability to the translation machinery, storage or degradation, depending on the associated proteins. These aggregates of mRNPs containing mRNAs that are not being translated colocalize in cytoplasmic foci, and their numbers and size vary according to cell conditions such as oxidative stress, nutritional status and treatment with drugs that inhibit translation.
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13
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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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14
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Differential Subcellular Localization of Leishmania Alba-Domain Proteins throughout the Parasite Development. PLoS One 2015; 10:e0137243. [PMID: 26334886 PMCID: PMC4559404 DOI: 10.1371/journal.pone.0137243] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/14/2015] [Indexed: 12/15/2022] Open
Abstract
Alba-domain proteins are RNA-binding proteins found in archaea and eukaryotes and recently studied in protozoan parasites where they play a role in the regulation of virulence factors and stage-specific proteins. This work describes in silico structural characterization, cellular localization and biochemical analyses of Alba-domain proteins in Leishmania infantum. We show that in contrast to other protozoa, Leishmania have two Alba-domain proteins, LiAlba1 and LiAlba3, representative of the Rpp20- and the Rpp25-like eukaryotic subfamilies, respectively, which share several sequence and structural similarities but also important differences with orthologs in other protozoa, especially in sequences targeted for post-translational modifications. LiAlba1 and LiAlba3 proteins form a complex interacting with other RNA-binding proteins, ribosomal subunits, and translation factors as supported by co-immunoprecipitation and sucrose gradient sedimentation analysis. A higher co-sedimentation of Alba proteins with ribosomal subunits was seen upon conditions of decreased translation, suggesting a role of these proteins in translational repression. The Leishmania Alba-domain proteins display differential cellular localization throughout the parasite development. In the insect promastigote stage, Alba proteins co-localize predominantly to the cytoplasm but they translocate to the nucleolus and the flagellum upon amastigote differentiation in the mammalian host and are found back to the cytoplasm once amastigote differentiation is completed. Heat-shock, a major signal of amastigote differentiation, triggers Alba translocation to the nucleolus and the flagellum. Purification of the Leishmania flagellum confirmed LiAlba3 enrichment in this organelle during amastigote differentiation. Moreover, partial characterization of the Leishmania flagellum proteome of promastigotes and differentiating amastigotes revealed the presence of other RNA-binding proteins, as well as differences in the flagellum composition between these two parasite lifestages. Shuttling of Alba-domain proteins between the cytoplasm and the nucleolus or the flagellum throughout the parasite life cycle suggests that these RNA-binding proteins participate in several distinct regulatory pathways controlling developmental gene expression in Leishmania.
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15
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Levy GV, Bañuelos CP, Níttolo AG, Ortiz GE, Mendiondo N, Moretti G, Tekiel VS, Sánchez DO. Depletion of the SR-Related Protein TbRRM1 Leads to Cell Cycle Arrest and Apoptosis-Like Death in Trypanosoma brucei. PLoS One 2015; 10:e0136070. [PMID: 26284933 PMCID: PMC4540419 DOI: 10.1371/journal.pone.0136070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 07/29/2015] [Indexed: 11/19/2022] Open
Abstract
Arginine-Serine (RS) domain-containing proteins are RNA binding proteins with multiple functions in RNA metabolism. In mammalian cells this group of proteins is also implicated in regulation and coordination of cell cycle and apoptosis. In trypanosomes, an early branching group within the eukaryotic lineage, this group of proteins is represented by 3 members, two of them are SR proteins and have been recently shown to be involved in rRNA processing as well as in pre-mRNA splicing and stability. Here we report our findings on the 3rd member, the SR-related protein TbRRM1. In the present study, we showed that TbRRM1 ablation by RNA-interference in T. brucei procyclic cells leads to cell-cycle block, abnormal cell elongation compatible with the nozzle phenotype and cell death by an apoptosis-like mechanism. Our results expand the role of the trypanosomal RS-domain containing proteins in key cellular processes such as cell cycle and apoptosis-like death, roles also carried out by the mammalian SR proteins, and thus suggesting a conserved function in this phylogenetically conserved protein family.
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Affiliation(s)
- Gabriela V. Levy
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
- * E-mail:
| | - Carolina P. Bañuelos
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
| | - Analía G. Níttolo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
| | - Gastón E. Ortiz
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
| | - Nicolás Mendiondo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
| | - Georgina Moretti
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
| | - Valeria S. Tekiel
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
| | - Daniel O. Sánchez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (IIB-UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 25 de Mayo y Francia. Gral. San Martín, Buenos Aires, Argentina
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16
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Michaeli S. The response of trypanosomes and other eukaryotes to ER stress and the spliced leader RNA silencing (SLS) pathway in Trypanosoma brucei. Crit Rev Biochem Mol Biol 2015; 50:256-67. [PMID: 25985970 DOI: 10.3109/10409238.2015.1042541] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The unfolded protein response (UPR) is induced when the quality control machinery of the cell is overloaded with unfolded proteins or when one of the functions of the endoplasmic reticulum (ER) is perturbed. Here, I describe UPR in yeast and mammals, and compare it to what we know about pathogenic fungi and the parasitic protozoans from the order kinetoplastida, focusing on the novel pathway the spliced leader silencing (SLS) in Trypanosoma brucei. Trypanosomes lack conventional transcription regulation, and thus, lack most of the UPR machinery present in other eukaryotes. Trypanosome genes are transcribed in polycistronic units that are processed by trans-splicing and polyadenylation. In trans-splicing, which is essential for processing of each mRNA, an exon known as the spliced leader (SL) is added to all mRNAs from a small RNA, the SL RNA. Under severe ER stress, T. brucei elicits the SLS pathway. In SLS, the transcription of the SL RNA gene is extinguished, and the entire transcription complex dissociates from the SL RNA promoter. Induction of SLS is mediated by an ER-associated kinase (PK3) that migrates to the nucleus, where it phosphorylates the TATA-binding protein (TRF4), leading shut-off of SL RNA transcription. As a result, trans-splicing is inhibited and the parasites activate a programmed cell death (PCD) pathway. Despite the ability to sense the ER stress, the different eukaryotes, especially unicellular parasites and pathogenic fungi, developed a variety of unique and different ways to sense and adjust to this stress in a manner different from their host.
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Affiliation(s)
- Shulamit Michaeli
- a The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University , Ramat-Gan , Israel
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17
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Pariona-Llanos R, Pavani RS, Reis M, Noël V, Silber AM, Armelin HA, Cano MIN, Elias MC. Glyceraldehyde 3-phosphate dehydrogenase-telomere association correlates with redox status in Trypanosoma cruzi. PLoS One 2015; 10:e0120896. [PMID: 25775131 PMCID: PMC4361584 DOI: 10.1371/journal.pone.0120896] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/27/2015] [Indexed: 01/04/2023] Open
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a classical metabolic enzyme involved in energy production and plays a role in additional nuclear functions, including transcriptional control, recognition of misincorporated nucleotides in DNA and maintenance of telomere structure. Here, we show that the recombinant protein T. cruzi GAPDH (rTcGAPDH) binds single-stranded telomeric DNA. We demonstrate that the binding of GAPDH to telomeric DNA correlates with the balance between oxidized and reduced forms of nicotinamide adenine dinucleotides (NAD+/NADH). We observed that GAPDH-telomere association and NAD+/NADH balance changed throughout the T. cruzi life cycle. For example, in replicative epimastigote forms of T. cruzi, which show similar intracellular concentrations of NAD+ and NADH, GAPDH binds to telomeric DNA in vivo and this binding activity is inhibited by exogenous NAD+. In contrast, in the T. cruzi non-proliferative trypomastigote forms, which show higher NAD+ concentration, GAPDH was absent from telomeres. In addition, NAD+ abolishes physical interaction between recombinant GAPDH and synthetic telomere oligonucleotide in a cell free system, mimicking exogenous NAD+ that reduces GAPDH-telomere interaction in vivo. We propose that the balance in the NAD+/NADH ratio during T. cruzi life cycle homeostatically regulates GAPDH telomere association, suggesting that in trypanosomes redox status locally modulates GAPDH association with telomeric DNA.
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Affiliation(s)
- Ricardo Pariona-Llanos
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, Brazil
| | - Raphael Souza Pavani
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, Brazil
| | - Marcelo Reis
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, Brazil
| | - Vincent Noël
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, Brazil
| | - Ariel Mariano Silber
- Unit for Drug Discovery—Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Hugo Aguirre Armelin
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Isabel Nogueira Cano
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho—UNESP, Botucatu, Brazil
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, Brazil
- * E-mail:
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18
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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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Stress induces changes in the phosphorylation of Trypanosoma cruzi RNA polymerase II, affecting its association with chromatin and RNA processing. EUKARYOTIC CELL 2014; 13:855-65. [PMID: 24813189 DOI: 10.1128/ec.00066-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The phosphorylation of the carboxy-terminal heptapeptide repeats of the largest subunit of RNA polymerase II (Pol II) controls several transcription-related events in eukaryotes. Trypanosomatids lack these typical repeats and display an unusual transcription control. RNA Pol II associates with the transcription site of the spliced leader (SL) RNA, which is used in the trans-splicing of all mRNAs transcribed on long polycistronic units. We found that Trypanosoma cruzi RNA Pol II associated with chromatin is highly phosphorylated. When transcription is inhibited by actinomycin D, the enzyme runs off from SL genes, remaining hyperphosphorylated and associated with polycistronic transcription units. Upon heat shock, the enzyme is dephosphorylated and remains associated with the chromatin. Transcription is partially inhibited with the accumulation of housekeeping precursor mRNAs, except for heat shock genes. DNA damage caused dephosphorylation and transcription arrest, with RNA Pol II dissociating from chromatin although staying at the SL. In the presence of calyculin A, the hyperphosphorylated form detached from chromatin, including the SL loci. These results indicate that in trypanosomes, the unusual RNA Pol II is phosphorylated during the transcription of SL and polycistronic operons. Different types of stresses modify its phosphorylation state, affecting pre-RNA processing.
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Abstract
Trypanosoma cruzi is the causal agent of Chagas' disease, a debilitating disorder affecting millions of people in several countries. A flagellated protozoan parasite, T. cruzi has a complex life cycle that involves infecting an insect and a mammalian host. During its life cycle, the parasite undergoes several kinds of stress, prominent among which is heat stress. To deal with this environmental challenge, molecular chaperones and proteases, also known as heat shock proteins (HSPs), are induced as part of the stress response. Several families of HSPs are synthesized by T. cruzi, including members of the major HSP classes such as HSP70, HSP90, HSP100, HSP40, chaperonins and small HSPs, and these proteins show conserved and unique features. In this review we describe these proteins and the corresponding gene expression patterns and discuss their relevance to the biology of the parasite.
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Affiliation(s)
- Turán P Urményi
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil,
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21
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Bernabó G, Levy G, Ziliani M, Caeiro LD, Sánchez DO, Tekiel V. TcTASV-C, a protein family in Trypanosoma cruzi that is predominantly trypomastigote-stage specific and secreted to the medium. PLoS One 2013; 8:e71192. [PMID: 23923058 PMCID: PMC3726618 DOI: 10.1371/journal.pone.0071192] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 06/27/2013] [Indexed: 12/20/2022] Open
Abstract
Among the several multigene families codified by the genome of T. cruzi, the TcTASV family was the latest discovered. The TcTASV (Trypomastigote, Alanine, Serine, Valine) family is composed of ∼40 members, with conserved carboxi- and amino-termini but with a variable central core. According to the length and sequence of the central region the family is split into 3 subfamilies. The TcTASV family is conserved in the genomes of – at least – lineages TcI and TcVI and has no orthologues in other trypanosomatids. In the present work we focus on the study of the TcTASV-C subfamily, composed by 16 genes in the CL Brener strain. We determined that TcTASV-C is preferentially expressed in trypomastigotes, but it is not a major component of the parasite. Both immunoflourescence and flow cytometry experiments indicated that TcTASV-C has a clonal expression, i.e. it is not expressed by all the parasites of a certain population at the same time. We also determined that TcTASV-C is phosphorylated and glycosylated. TASV-C is attached to the parasite surface by a GPI anchor and is shed spontaneously into the medium. About 30% of sera from infected hosts reacted with TcTASV-C, confirming its exposition to the immune system. Its superficial localization and secretory nature suggest a possible role in host-parasite interactions.
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Affiliation(s)
- Guillermo Bernabó
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomus (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gabriela Levy
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomus (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Ziliani
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomus (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucas D. Caeiro
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomus (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Daniel O. Sánchez
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomus (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Valeria Tekiel
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomus (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
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Fernández-Moya SM, García-Pérez A, Kramer S, Carrington M, Estévez AM. Alterations in DRBD3 ribonucleoprotein complexes in response to stress in Trypanosoma brucei. PLoS One 2012; 7:e48870. [PMID: 23145003 PMCID: PMC3493610 DOI: 10.1371/journal.pone.0048870] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/01/2012] [Indexed: 12/27/2022] Open
Abstract
Regulation of RNA polymerase II transcription initiation is apparently absent in trypanosomes. Instead, these eukaryotes control gene expression mainly at the post-transcriptional level. Regulation is exerted through the action of numerous RNA-binding proteins that modulate mRNA processing, turnover, translation and localization. In this work we show that the RNA-binding protein DRBD3 resides in the cytoplasm, but localizes to the nucleus upon oxidative challenge and to stress granules under starvation conditions. DRBD3 associates with other proteins to form a complex, the composition of which is altered by cellular stress. Interestingly, target mRNAs remain bound to DRBD3 under stress conditions. Our results suggest that DRBD3 transports regulated mRNAs within the cell in the form of ribonucleoprotein complexes that are remodeled in response to environmental cues.
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Affiliation(s)
| | - Angélica García-Pérez
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Armilla, Granada, Spain
| | - Susanne Kramer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Antonio M. Estévez
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Armilla, Granada, Spain
- * E-mail:
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Názer E, Verdún RE, Sánchez DO. Severe heat shock induces nucleolar accumulation of mRNAs in Trypanosoma cruzi. PLoS One 2012; 7:e43715. [PMID: 22952745 PMCID: PMC3428281 DOI: 10.1371/journal.pone.0043715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 07/26/2012] [Indexed: 12/12/2022] Open
Abstract
Several lines of evidence have shown that, besides its traditional function in ribosome biogenesis, the nucleolus is also involved in regulating other cellular processes such as mRNA metabolism, and that it also plays an important role as a sensor and coordinator of the stress response. We have recently shown that a subset of RNA Binding Proteins and the poly(A)+ RNA are accumulated into the Trypanosoma cruzi nucleolus after inducing transcription inhibition with Actinomycin D. In this study, we investigated the behaviour of the T. cruzi mRNA population in parasites subjected to severe heat shock, an environmental stress that also decreases the rate of RNA synthesis. We found that the bulk of poly(A)+ RNA is reversibly accumulated into the nucleolus when exposing T. cruzi epimastigote forms to severe heat shock. However, the Hsp70 mRNA was able to bypass such nucleolar accumulation. Together, these data reinforce the idea about the involvement of the T. cruzi nucleolus in mRNA metabolism during an environmental stress response. Interestingly, T. brucei procyclic forms did not induce nucleolar accumulation of poly(A)+ RNA under such stress condition, suggesting that different trypanosomatids have adopted different responses to deal with the same stress conditions.
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Affiliation(s)
- Ezequiel Názer
- Instituto de Investigaciones Biotecnológicas - UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
| | - Ramiro E. Verdún
- Leonard M. Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Daniel O. Sánchez
- Instituto de Investigaciones Biotecnológicas - UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
- * E-mail:
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Názer E, Sánchez DO. Nucleolar accumulation of RNA binding proteins induced by Actinomycin D is functional in Trypanosoma cruzi and Leishmania mexicana but not in T. brucei. PLoS One 2011; 6:e24184. [PMID: 21904613 PMCID: PMC3164162 DOI: 10.1371/journal.pone.0024184] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/01/2011] [Indexed: 12/24/2022] Open
Abstract
We have recently shown in T. cruzi that a group of RNA Binding Proteins (RBPs), involved in mRNA metabolism, are accumulated into the nucleolus in response to Actinomycin D (ActD) treatment. In this work, we have extended our analysis to other members of the trypanosomatid lineage. In agreement with our previous study, the mechanism seems to be conserved in L. mexicana, since both endogenous RBPs and a transgenic RBP were relocalized to the nucleolus in parasites exposed to ActD. In contrast, in T. brucei, neither endogenous RBPs (TbRRM1 and TbPABP2) nor a transgenic RBP from T. cruzi were accumulated into the nucleolus under such treatment. Interestingly, when a transgenic TbRRM1was expressed in T. cruzi and the parasites exposed to ActD, TbRRM1 relocated to the nucleolus, suggesting that it contains the necessary sequence elements to be targeted to the nucleolus. Together, both experiments demonstrate that the mechanism behind nucleolar localization of RBPs, which is present in T. cruzi and L. mexicana, is not functional in T. brucei, suggesting that it has been lost or retained differentially during the evolution of the trypanosomatid lineage.
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Affiliation(s)
- Ezequiel Názer
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
| | - Daniel O. Sánchez
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús, UNSAM-CONICET, San Martín, Provincia de Buenos Aires, Argentina
- * E-mail:
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