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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: 7] [Impact Index Per Article: 0.9] [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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Wei L, Wang Q, Wu H, Ji C, Zhao J. Proteomic and metabolomic responses of Pacific oyster Crassostrea gigas to elevated pCO2 exposure. J Proteomics 2015; 112:83-94. [DOI: 10.1016/j.jprot.2014.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 08/11/2014] [Indexed: 01/11/2023]
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Jäger AV, De Gaudenzi JG, Cassola A, D'Orso I, Frasch AC. mRNA maturation by two-step trans-splicing/polyadenylation processing in trypanosomes. Proc Natl Acad Sci U S A 2007; 104:2035-42. [PMID: 17267594 PMCID: PMC1892994 DOI: 10.1073/pnas.0611125104] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Indexed: 11/18/2022] Open
Abstract
Trypanosomes are unique eukaryotic cells, in that they virtually lack mechanisms to control gene expression at the transcriptional level. These microorganisms mostly control protein synthesis by posttranscriptional regulation processes, like mRNA stabilization and degradation. Transcription in these cells is polycistronic. Tens to hundreds of protein-coding genes of unrelated function are arrayed in long clusters on the same DNA strand. Polycistrons are cotranscriptionally processed by trans-splicing at the 5' end and polyadenylation at the 3' end, generating monocistronic units ready for degradation or translation. In this work, we show that some trans-splicing/polyadenylation sites may be skipped during normal polycistronic processing. As a consequence, dicistronic units or monocistronic transcripts having long 3' UTRs are produced. Interestingly, these unspliced transcripts can be processed into mature mRNAs by the conventional trans-splicing/polyadenylation events leading to translation. To our knowledge, this is a previously undescribed mRNA maturation by trans-splicing uncoupled from transcription. We identified an RNA-recognition motif-type protein, homologous to the mammalian polypyrimidine tract-binding protein, interacting with one of the partially processed RNAs analyzed here that might be involved in exon skipping. We propose that splice-site skipping might be part of a posttranscriptional mechanism to regulate gene expression in trypanosomes, through the generation of premature nontranslatable RNA molecules.
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Affiliation(s)
- Adriana V. Jäger
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Javier G. De Gaudenzi
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Alejandro Cassola
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Iván D'Orso
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
| | - Alberto C. Frasch
- Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico Chascomus, Universidad Nacional de San Martín–Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Gral. Paz 5445, Edificio 24, INTI, 1650 San Martín, Provincia de Buenos Aires, Argentina
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Coelho ER, Rodrigues DDC, Urményi TP, Rondinelli E, Silva R. Polymorphic and differential expression of the Trypanosoma cruzi alleles containing universal minicircle binding protein. Biochem Biophys Res Commun 2006; 341:382-90. [PMID: 16414010 DOI: 10.1016/j.bbrc.2005.12.189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 12/27/2005] [Indexed: 01/23/2023]
Abstract
DNA replication mechanisms are poorly understood in most of trypanosomatids, in particular the replication of the peculiar mitochondrial DNA, the kinetoplast DNA (kDNA). To contribute to the knowledge on the mechanism of kDNA replication in Trypanosoma cruzi, we have previously characterized the Universal Minicircle Sequence Binding Protein of this parasite (TcUMSBP), which was first called PDZ5 [E.R. Coelho, T.P. Urmenyi, J. Franco da Silveira, E. Rondinelli, R. Silva, Identification of PDZ5, a candidate universal minicircle sequence binding protein of Trypanosoma cruzi, Int. J. Parasitol. 33 (2003) 853-858]. In this work, we describe two highly polymorphic alleles of the TcUMSBP locus in the T. cruzi reference clone CL Brener and the differential expression pattern of these alleles. A 62 bp sequence in the TcUMSBP upstream intergenic region in one of its alleles affects the efficiency of polycistronic RNA processing and the polyadenylation sites, and therefore regulates the differential expression of TcUMSBP alleles of this locus.
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Affiliation(s)
- Elielton R Coelho
- Instituto de Biofísica Carlos Chagas Filho, CCS, Bloco G, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21949-900, Brazil
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Vanchinathan P, Brewer JL, Harb OS, Boothroyd JC, Singh U. Disruption of a locus encoding a nucleolar zinc finger protein decreases tachyzoite-to-bradyzoite differentiation in Toxoplasma gondii. Infect Immun 2005; 73:6680-8. [PMID: 16177345 PMCID: PMC1230886 DOI: 10.1128/iai.73.10.6680-6688.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During its life cycle in intermediate hosts, Toxoplasma gondii exists in two interconverting developmental stages: tachyzoites and bradyzoites. This interconversion is essential for the survival and pathogenicity of the parasite, but little is known about the genetic mechanisms that control this process. We have previously generated tachyzoite-to-bradyzoite differentiation (Tbd(-)) mutants using chemical mutagenesis and a green fluorescent protein-based selection strategy. The genetic loci responsible for the Tbd(-) phenotype, however, could not be identified. We have now used an insertional mutagenesis strategy to generate two differentiation mutants: TBD-5 and TBD-6 that switch to bradyzoites at 10 and 50% of wild-type levels, respectively. In TBD-6 there is a single insertion of the mutagenesis vector 164 bp upstream of the transcription start site of a gene encoding a zinc finger protein (ZFP1). Disruption of this locus in wild-type parasites reproduces the decreased stage conversion phenotype. ZFP1 is targeted to the parasite nucleolus by CCHC motifs and significantly altered expression levels are toxic to the parasites. This represents the first identification of a gene necessary for efficient conversion of tachyzoites to bradyzoites.
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Affiliation(s)
- Padmini Vanchinathan
- Department of Internal Medicine, Division of Infectious Diseases, Stanford University School of Medicine, California 94305-5124, USA
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Coelho ER, Urményi TP, Franco da Silveira J, Rondinelli E, Silva R. Identification of PDZ5, a candidate universal minicircle sequence binding protein of Trypanosoma cruzi. Int J Parasitol 2003; 33:853-8. [PMID: 12865085 DOI: 10.1016/s0020-7519(03)00107-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The dodecamer universal minicircle sequence is a conserved sequence present in minicircles of trypanosomatid kinetoplast DNA studied so far. This sequence is recognised by a protein named universal minicircle sequence binding protein, described for Crithidia fasciculata, involved in minicircle DNA replication. We have identified a Trypanosoma cruzi gene homologue of the Crithidia fasciculata universal minicircle sequence binding protein. Similar to the Crithidia fasciculata universal minicircle sequence binding protein, the Trypanosoma cruzi protein, named PDZ5, contains five zinc finger motifs. Pulsed field gel electrophoresis indicated that the pdz5 gene is located in the chromosomal band XX of the Trypanosoma cruzi genome. The predicted amino acid sequence of PDZ5 shows a high degree of similarity with several trypanosomatid zinc finger proteins. Specific antibody raised against Crithidia fasciculata universal minicircle sequence binding protein recognises both the recombinant and endogenous PDZ5. The complete pdz5 coding sequence cloned in bacteria expresses a recombinant PDZ5 protein that binds specifically to the universal minicircle sequence dodecamer. These data strongly suggest that PDZ5 represents a Trypanosoma cruzi universal minicircle sequence binding protein.
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Affiliation(s)
- Elielton R Coelho
- Programa de Biologia Molecular, Instituto de Biofísica Carlos Chagas Filho, CCS, bloco G Universidade Federal de Rio de Janeiro, 21949-900 Rio de Janeiro, Brazil
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Paugam A, Bulteau AL, Dupouy-Camet J, Creuzet C, Friguet B. Characterization and role of protozoan parasite proteasomes. Trends Parasitol 2003; 19:55-9. [PMID: 12586468 DOI: 10.1016/s1471-4922(02)00064-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The proteasome, a large non-lysosomal multi-subunit protease complex, is ubiquitous in eukaryotic cells. In protozoan parasites, the proteasome is involved in cell differentiation and replication, and could therefore be a promising therapeutic target. This article reviews the present knowledge of proteasomes in protozoan parasites of medical importance such as Giardia, Entamoeba, Leishmania, Trypanosoma, Plasmodium and Toxoplasma spp.
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Affiliation(s)
- André Paugam
- Laboratoire Signalisation et Parasites (EA 3623), Université Paris 5, C.H.U. Cochin, 27, rue du Faubourg Saint Jacques 75014 Paris, France.
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