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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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Conserved Curvature of RNA Polymerase I Core Promoter Beyond rRNA Genes: The Case of the Tritryps. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 13:355-63. [PMID: 26718450 PMCID: PMC4747651 DOI: 10.1016/j.gpb.2015.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/17/2015] [Accepted: 09/24/2015] [Indexed: 11/23/2022]
Abstract
In trypanosomatids, the RNA polymerase I (RNAPI)-dependent promoters controlling the ribosomal RNA (rRNA) genes have been well identified. Although the RNAPI transcription machinery recognizes the DNA conformation instead of the DNA sequence of promoters, no conformational study has been reported for these promoters. Here we present the in silico analysis of the intrinsic DNA curvature of the rRNA gene core promoters in Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. We found that, in spite of the absence of sequence conservation, these promoters hold conformational properties similar to other eukaryotic rRNA promoters. Our results also indicated that the intrinsic DNA curvature pattern is conserved within the Leishmania genus and also among strains of T. cruzi and T. brucei. Furthermore, we analyzed the impact of point mutations on the intrinsic curvature and their impact on the promoter activity. Furthermore, we found that the core promoters of protein-coding genes transcribed by RNAPI in T. brucei show the same conserved conformational characteristics. Overall, our results indicate that DNA intrinsic curvature of the rRNA gene core promoters is conserved in these ancient eukaryotes and such conserved curvature might be a requirement of RNAPI machinery for transcription of not only rRNA genes but also protein-coding genes.
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Shaw J, Pratlong F, Floeter-Winter L, Ishikawa E, El Baidouri F, Ravel C, Dedet JP. Characterization of Leishmania (Leishmania) waltoni n.sp. (Kinetoplastida: Trypanosomatidae), the Parasite Responsible for Diffuse Cutaneous Leishmaniasis in the Dominican Republic. Am J Trop Med Hyg 2015; 93:552-8. [PMID: 26149864 DOI: 10.4269/ajtmh.14-0774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/19/2015] [Indexed: 11/07/2022] Open
Abstract
Leishmania parasites isolated, between 1979 and 1988 by the late Bryce Walton, from Dominican Republic (DR) patients with diffuse cutaneous leishmaniasis, were characterized using a panel of 12 isoenzymes, 23 monoclonal antibodies, small subunit ribosomal DNA (SSu rDNA), and multilocus sequence analysis (MLSA). The isoenzyme and monoclonal antibody profiles and the MLSA results showed that the Dominican Republic parasites were distinct from other described Leishmania species. This new species belongs to the mexicana complex, which is distributed in central and parts of northern South America. It is suggested that the parasites uniqueness from other members of the mexicana complex is related to it being isolated on an island for millions of years. If Leishmania (Leishmania) waltoni fails to adapt to some imported mammal, such as the house rat, it will be the only Leishmania to be classified as an endangered species. The excessive destruction of habitats on Hispaniola threatens the survival of its vectors and presumed natural reservoirs, such as the rodent hutias and the small insectivorous mammal solenodon. The concept of Leishmania species is discussed in the light of recent evaluations on criteria for defining bacterial species.
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Affiliation(s)
- Jeffrey Shaw
- Parasitology Department, Biomedical Sciences Institute, São Paulo University, São Paulo, Brazil; French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France; Biology Department, BioSciences Institute, São Paulo University, São Paulo, Brazil; Tropical Medicine Nucleus, Pará Federal University, Brazil; School of Life Sciences, University of Lincoln, Lincoln, England
| | - Francine Pratlong
- Parasitology Department, Biomedical Sciences Institute, São Paulo University, São Paulo, Brazil; French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France; Biology Department, BioSciences Institute, São Paulo University, São Paulo, Brazil; Tropical Medicine Nucleus, Pará Federal University, Brazil; School of Life Sciences, University of Lincoln, Lincoln, England
| | - Lucile Floeter-Winter
- Parasitology Department, Biomedical Sciences Institute, São Paulo University, São Paulo, Brazil; French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France; Biology Department, BioSciences Institute, São Paulo University, São Paulo, Brazil; Tropical Medicine Nucleus, Pará Federal University, Brazil; School of Life Sciences, University of Lincoln, Lincoln, England
| | - Edna Ishikawa
- Parasitology Department, Biomedical Sciences Institute, São Paulo University, São Paulo, Brazil; French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France; Biology Department, BioSciences Institute, São Paulo University, São Paulo, Brazil; Tropical Medicine Nucleus, Pará Federal University, Brazil; School of Life Sciences, University of Lincoln, Lincoln, England
| | - Fouad El Baidouri
- Parasitology Department, Biomedical Sciences Institute, São Paulo University, São Paulo, Brazil; French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France; Biology Department, BioSciences Institute, São Paulo University, São Paulo, Brazil; Tropical Medicine Nucleus, Pará Federal University, Brazil; School of Life Sciences, University of Lincoln, Lincoln, England
| | - Christophe Ravel
- Parasitology Department, Biomedical Sciences Institute, São Paulo University, São Paulo, Brazil; French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France; Biology Department, BioSciences Institute, São Paulo University, São Paulo, Brazil; Tropical Medicine Nucleus, Pará Federal University, Brazil; School of Life Sciences, University of Lincoln, Lincoln, England
| | - Jean-Pierre Dedet
- Parasitology Department, Biomedical Sciences Institute, São Paulo University, São Paulo, Brazil; French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France; Biology Department, BioSciences Institute, São Paulo University, São Paulo, Brazil; Tropical Medicine Nucleus, Pará Federal University, Brazil; School of Life Sciences, University of Lincoln, Lincoln, England
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Hernández R, Cevallos AM. Ribosomal RNA gene transcription in trypanosomes. Parasitol Res 2014; 113:2415-24. [PMID: 24828347 DOI: 10.1007/s00436-014-3940-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/01/2014] [Indexed: 11/30/2022]
Abstract
Leishmania major, Trypanosoma cruzi and Trypanosoma brucei are pathogenic species from the order Kinetoplastida. The molecular and cellular studies of parasites, such as of the biosynthesis of essential macromolecules, are important in designing successful strategies for control. A major stage in ribosome biogenesis is the transcription of genes encoding ribosomal (r)RNA. These genes are transcribed in trypanosome cells by RNA polymerase I, similar to what occurs in all eukaryotes analysed to date. In addition, and most remarkably, the African species, T. brucei, transcribe their major cell surface protein genes using this class of polymerase. Since its discovery, the research interest in this phenomenon has been overwhelming; therefore, analysis of the canonical, yet essential, transcription of rRNA has been comparatively neglected. In this work, a review of rRNA gene transcription and data on gene promoter structures, transcription machineries and epigenetic conditions is presented for trypanosomatids. Because species-specific molecules represent potential targets for chemotherapy, their existence within trypanosomes is highlighted.
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Affiliation(s)
- Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad Universitaria, 04510, México, D.F., Mexico,
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Smircich P, Forteza D, El-Sayed NM, Garat B. Genomic analysis of sequence-dependent DNA curvature in Leishmania. PLoS One 2013; 8:e63068. [PMID: 23646176 PMCID: PMC3639952 DOI: 10.1371/journal.pone.0063068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 03/27/2013] [Indexed: 11/26/2022] Open
Abstract
Leishmania major is a flagellated protozoan parasite of medical importance. Like other members of the Trypanosomatidae family, it possesses unique mechanisms of gene expression such as constitutive polycistronic transcription of directional gene clusters, gene amplification, mRNA trans-splicing, and extensive editing of mitochondrial transcripts. The molecular signals underlying most of these processes remain under investigation. In order to investigate the role of DNA secondary structure signals in gene expression, we carried out a genome-wide in silico analysis of the intrinsic DNA curvature. The L. major genome revealed a lower frequency of high intrinsic curvature regions as well as inter- and intra- chromosomal distribution heterogeneity, when compared to prokaryotic and eukaryotic organisms. Using a novel method aimed at detecting region-integrated intrinsic curvature (RIIC), high DNA curvature was found to be associated with regions implicated in transcription initiation. Those include divergent strand-switch regions between directional gene clusters and regions linked to markers of active transcription initiation such as acetylated H3 histone, TRF4 and SNAP50. These findings suggest a role for DNA curvature in transcription initiation in Leishmania supporting the relevance of DNA secondary structures signals.
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Affiliation(s)
- Pablo Smircich
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Montevideo, Uruguay
- Departamento de Genética, Facultad de Medicina, Montevideo, Uruguay
| | - Diego Forteza
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Montevideo, Uruguay
| | - Najib M. El-Sayed
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland College Park, Maryland, United States of America
| | - Beatriz Garat
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Montevideo, Uruguay
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Orlando TC, Mayer MG, Campbell DA, Sturm NR, Floeter-Winter LM. RNA polymerase I promoter and splice acceptor site recognition affect gene expression in non-pathogenic Leishmania species. Mem Inst Oswaldo Cruz 2007; 102:891-4. [PMID: 18060313 DOI: 10.1590/s0074-02762007005000123] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Accepted: 10/22/2007] [Indexed: 11/22/2022] Open
Abstract
Leishmania (Sauroleishmania) tarentolae has biotechnological potential for use as live vaccine against visceral leishmaniasis and as a system for the over expression of eukaryotic proteins that possess accurate post-translational modifications. For both purposes, new systems for protein expression in this non-pathogenic protozoan are necessary. The ribosomal RNA promoter proved to be a stronger transcription driver since its use yielded increased levels of recombinant protein in organisms of both genera Trypanosoma or Leishmania. We have evaluated heterologous expression systems using vectors with two different polypyrimidine tracts in the splice acceptor site by measuring a reporter gene transcribed from L. tarentolae RNA polymerase I promoter. Our data indicate that the efficiency of chloramphenicol acetyl transferase expression changed drastically with homologous or heterologous sequences, depending on the polypyrimidine tract used in the construct and differences in size and/or distance from the AG dinucleotide. In relation to the promoter sequence the reporter expression was higher in heterologous lizard-infecting species than in the homologous L. tarentolae or in the mammalian-infecting L. (Leishmania) amazonensis.
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Figueroa-Angulo E, María Cevallos A, Zentella A, López-Villaseñor I, Hernández R. Potential regulatory elements in the Trypanosoma cruzi rRNA gene promoter. ACTA ACUST UNITED AC 2006; 1759:497-501. [PMID: 17050002 DOI: 10.1016/j.bbaexp.2006.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 09/13/2006] [Accepted: 09/14/2006] [Indexed: 11/30/2022]
Abstract
The Trypanosoma cruzi rRNA gene promoter was characterized by deletion and point mutation analyses. A core of 89 bp was identified as the minimal region with full promoter activity. This core region is flanked upstream by a control element that stimulates its activity, and downstream by a novel down regulating region of about 200 bp. A point mutation analysis of the transcription start region evidenced 7 contiguous nucleotides where individual substitutions produced in all cases a defective promoter. It is generally accepted that the anciently speciated trypanosomatids lack strict promoters for protein coding genes transcribed by RNA polymerase II. The occurrence of a well structured rRNA gene promoter in these species suggests an early appearance of the RNA polymerase I promoters in the evolution of eukaryotic cells.
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Affiliation(s)
- Elisa Figueroa-Angulo
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70-228, 04510 México DF, Mexico
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