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Kaur D, Agrahari M, Bhattacharya A, Bhattacharya S. The non-LTR retrotransposons of Entamoeba histolytica: genomic organization and biology. Mol Genet Genomics 2022; 297:1-18. [PMID: 34999963 DOI: 10.1007/s00438-021-01843-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/26/2021] [Indexed: 11/24/2022]
Abstract
Genome sequence analysis of Entamoeba species revealed various classes of transposable elements. While E. histolytica and E. dispar are rich in non-long terminal repeat (LTR) retrotransposons, E. invadens contains predominantly DNA transposons. Non-LTR retrotransposons of E. histolytica constitute three families of long interspersed nuclear elements (LINEs), and their short, nonautonomous partners, SINEs. They occupy ~ 11% of the genome. The EhLINE1/EhSINE1 family is the most abundant and best studied. EhLINE1 is 4.8 kb, with two ORFs that encode functions needed for retrotransposition. ORF1 codes for the nucleic acid-binding protein, and ORF2 has domains for reverse transcriptase (RT) and endonuclease (EN). Most copies of EhLINEs lack complete ORFs. ORF1p is expressed constitutively, but ORF2p is not detected. Retrotransposition could be demonstrated upon ectopic over expression of ORF2p, showing that retrotransposition machinery is functional. The newly retrotransposed sequences showed a high degree of recombination. In transcriptomic analysis, RNA-Seq reads were mapped to individual EhLINE1 copies. Although full-length copies were transcribed, no full-length 4.8 kb transcripts were seen. Rather, sense transcripts mapped to ORF1, RT and EN domains. Intriguingly, there was strong antisense transcription almost exclusively from the RT domain. These unique features of EhLINE1 could serve to attenuate retrotransposition in E. histolytica.
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Ribeiro YC, Robe LJ, Veluza DS, Dos Santos CMB, Lopes ALK, Krieger MA, Ludwig A. Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons. Mob DNA 2019; 10:34. [PMID: 31391870 PMCID: PMC6681497 DOI: 10.1186/s13100-019-0175-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/15/2019] [Indexed: 01/04/2023] Open
Abstract
Background Kinetoplastids are a flagellated group of protists, including some parasites, such as Trypanosoma and Leishmania species, that can cause diseases in humans and other animals. The genomes of these species enclose a fraction of retrotransposons including VIPER and TATE, two poorly studied transposable elements that encode a tyrosine recombinase (YR) and were previously classified as DIRS elements. This study investigated the distribution and evolution of VIPER and TATE in kinetoplastids to understand the relationships of these elements with other retrotransposons. Results We observed that VIPER and TATE have a discontinuous distribution among Trypanosomatidae, with several events of loss and degeneration occurring during a vertical transfer evolution. We were able to identify the terminal repeats of these elements for the first time, and we showed that these elements are potentially active in some species, including T. cruzi copies of VIPER. We found that VIPER and TATE are strictly related elements, which were named in this study as VIPER-like. The reverse transcriptase (RT) tree presented a low resolution, and the origin and relationships among YR groups remain uncertain. Conversely, for RH, VIPER-like grouped with Hepadnavirus, whereas for YR, VIPER-like sequences constituted two different clades that are closely allied to Crypton. Distinct topologies among RT, RH and YR trees suggest ancient rearrangements/exchanges in domains and a modular pattern of evolution with putative independent origins for each ORF. Conclusions Due to the presence of both elements in Bodo saltans, a nontrypanosomatid species, we suggested that VIPER and TATE have survived and remained active for more than 400 million years or were reactivated during the evolution of the host species. We did not find clear evidence of independent origins of VIPER-like from the other YR retroelements, supporting the maintenance of the DIRS group of retrotransposons. Nevertheless, according to phylogenetic findings and sequence structure obtained by this study and other works, we proposed separating DIRS elements into four subgroups: DIRS-like, PAT-like, Ngaro-like, and VIPER-like. Electronic supplementary material The online version of this article (10.1186/s13100-019-0175-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yasmin Carla Ribeiro
- 1Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Lizandra Jaqueline Robe
- 2Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, RS Brazil
| | | | | | - Ana Luisa Kalb Lopes
- 1Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, PR Brazil
| | | | - Adriana Ludwig
- 4Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR Brazil
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Pavia PX, Thomas MC, López MC, Puerta CJ. Molecular characterization of the short interspersed repetitive element SIRE in the six discrete typing units (DTUs) of Trypanosoma cruzi. Exp Parasitol 2012; 132:144-50. [PMID: 22750455 DOI: 10.1016/j.exppara.2012.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 06/06/2012] [Accepted: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Repetitive sequences constitute an important proportion of the Trypanosoma cruzi genome; hence, they have been used as molecular markers and as amplification targets to identify the parasite presence via PCR. In this study, a molecular characterization of the SIRE repetitive element was performed in the six discrete typing units (DTUs) of T. cruzi. The results evidenced that this element, located in multiple chromosomes, was interspersed in the genome of all DTUs of the parasite. The presence of several motifs implicated in element insertion, duplication, and functionality suggests that SIRE could be an active element in the parasite genome. Of interest, there were SIRE specific Alu I fragments that allowed to discriminate DTU I from the others DTUs. Moreover, an UPGMA phenetic tree constructed from fragment sharing Southern blot data showed that T. cruzi I isolates conform a cluster separated from the T. cruzi II-VI isolates. When the relative number of SIRE copies was determined, a variation from 105 to 2,000 copies per haploid genome was observed among the different isolates without kept a DTU-relationship. In all, these findings suggest that SIRE sequence is a good target for parasite DNA amplification.
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Affiliation(s)
- Paula X Pavia
- Laboratorio de Parasitología Molecular, Pontificia Universidad Javeriana, Carrera 7 No 43-82,Edificio Félix Restrepo, Oficina 608, Bogotá, Colombia.
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Caetano BC, Carmo BB, Melo MB, Cerny A, dos Santos SL, Bartholomeu DC, Golenbock DT, Gazzinelli RT. Requirement of UNC93B1 reveals a critical role for TLR7 in host resistance to primary infection with Trypanosoma cruzi. THE JOURNAL OF IMMUNOLOGY 2011; 187:1903-11. [PMID: 21753151 DOI: 10.4049/jimmunol.1003911] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
UNC93B1 associates with TLR3, 7, and 9, mediating their translocation from the endoplasmic reticulum to the endolysosome, thus allowing proper activation by microbial nucleic acids. We found that the triple-deficient 3d mice, which lack functional UNC93B1 as well as functional endosomal TLRs, are highly susceptible to infection with Trypanosoma cruzi. The enhanced parasitemia and mortality in 3d animals were associated with impaired proinflammatory response, including reduced levels of IL-12p40 and IFN-γ. Importantly, the phenotype of 3d mice was intermediary between MyD88(-/-) (highly susceptible) and TLR9(-/-) (moderately susceptible), indicating the involvement of an additional UN93B1-dependent TLR(s) on host resistance to T. cruzi. Hence, our experiments also revealed that TLR7 is a critical innate immune receptor involved in recognition of parasite RNA, induction of IL-12p40 by dendritic cells, and consequent IFN-γ by T lymphocytes. Furthermore, we show that upon T. cruzi infection, triple TLR3/7/9(-/-) mice had similar phenotype than 3d mice. These data imply that the nucleic acid-sensing TLRs are critical determinants of host resistance to primary infection with T. cruzi.
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Affiliation(s)
- Braulia C Caetano
- Division of Infectious Disease and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Thomas MC, Macias F, Alonso C, López MC. The biology and evolution of transposable elements in parasites. Trends Parasitol 2010; 26:350-62. [PMID: 20444649 DOI: 10.1016/j.pt.2010.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 03/30/2010] [Accepted: 04/01/2010] [Indexed: 12/19/2022]
Abstract
Transposable elements (TEs) are dynamic elements that can reshape host genomes by generating rearrangements with the potential to create or disrupt genes, to shuffle existing genes, and to modulate their patterns of expression. In the genomes of parasites that infect mammals several TEs have been identified that probably have been maintained throughout evolution due to their contribution to gene function and regulation of gene expression. This review addresses how TEs are organized, how they colonize the genomes of mammalian parasites, the functional role these elements play in parasite biology, and the interactions between these elements and the parasite genome.
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Affiliation(s)
- M Carmen Thomas
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra - CSIC, Parque Tecnológico de Ciencias de la Salud, 18100 Granada, Spain
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Brandão A, Jiang T. The composition of untranslated regions in Trypanosoma cruzi genes. Parasitol Int 2009; 58:215-9. [PMID: 19505588 DOI: 10.1016/j.parint.2009.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Revised: 05/26/2009] [Accepted: 06/01/2009] [Indexed: 11/25/2022]
Abstract
We collected the UTRs from Trypanosomacruzi genes that have been experimentally mapped and are publicly available, and made a comprehensive analysis of their composition features including sequence length, G+C content and relationship to ORF, composition of the most frequent words, and distribution of Simple Sequence Repeats (SSR). T. cruzi UTRs exhibit range length of 10-400bp for 5' UTR and 17-2800 for 3' UTR. Both UTRs display mean G+C content of 40%. Ratios between the UTR and protein coding segments show that the 5' UTR is limited to a maximum of 20% of the total length in the final transcript. The 5' UTR most frequent words in the range 4-12 bases are almost exact complement to the 3' UTR respective words. SSR in 3' UTR are longer than in 5' UTR and are mostly derived from TA/AT, TG/GT, and TTA/ATT. SSR accounts up to 20% of the nucleotide composition in 5' UTR and up to 90% in the 3' UTR.
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Bartholomeu DC, Ropert C, Melo MB, Parroche P, Junqueira CF, Teixeira SMR, Sirois C, Kasperkovitz P, Knetter CF, Lien E, Latz E, Golenbock DT, Gazzinelli RT. Recruitment and endo-lysosomal activation of TLR9 in dendritic cells infected with Trypanosoma cruzi. THE JOURNAL OF IMMUNOLOGY 2008; 181:1333-44. [PMID: 18606688 DOI: 10.4049/jimmunol.181.2.1333] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
TLR9 is critical in parasite recognition and host resistance to experimental infection with Trypanosoma cruzi. However, no information is available regarding nucleotide sequences and cellular events involved on T. cruzi recognition by TLR9. In silico wide analysis associated with in vitro screening of synthetic oligonucleotides demonstrates that the retrotransposon VIPER elements and mucin-like glycoprotein (TcMUC) genes in the T. cruzi genome are highly enriched for CpG motifs that are immunostimulatory for mouse and human TLR9, respectively. Importantly, infection with T. cruzi triggers high levels of luciferase activity under NF-kappaB-dependent transcription in HEK cells cotransfected with human TLR9, but not in control (cotransfected with human MD2/TLR4) HEK cells. Further, we observed translocation of TLR9 to the lysosomes during invasion/uptake of T. cruzi parasites by dendritic cells. Consistently, potent proinflammatory activity was observed when highly unmethylated T. cruzi genomic DNA was delivered to the endo-lysosomal compartment of host cells expressing TLR9. Thus, together our results indicate that the unmethylated CpG motifs found in the T. cruzi genome are likely to be main parasite targets and probably become available to TLR9 when parasites are destroyed in the lysosome-fused vacuoles during parasite invasion/uptake by phagocytes.
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Affiliation(s)
- Daniella C Bartholomeu
- Department of Parasitology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Role of transposable elements in trypanosomatids. Microbes Infect 2008; 10:575-81. [PMID: 18467144 DOI: 10.1016/j.micinf.2008.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 02/08/2008] [Indexed: 11/20/2022]
Abstract
Transposable elements constitute 2-5% of the genome content in trypanosomatid parasites. Some of them are involved in critical cellular functions, such as the regulation of gene expression in Leishmania spp. In this review, we highlight the remarkable role extinct transposable elements can play as the source of potential new functions.
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Pavia PX, Vallejo GA, Montilla M, Nicholls RS, Puerta CJ. Detection of Trypanosoma cruzi and Trypanosoma rangeli infection in triatomine vectors by amplification of the histone H2A/SIRE and the sno-RNA-C11 genes. Rev Inst Med Trop Sao Paulo 2007; 49:23-30. [PMID: 17384816 DOI: 10.1590/s0036-46652007000100005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 08/15/2006] [Indexed: 11/22/2022] Open
Abstract
Trypanosoma rangeli is non pathogenic for humans but of important medical and epidemiological interest because it shares vertebrate hosts, insect vectors, reservoirs and geographic areas with T. cruzi, the etiological agent of Chagas disease. Therefore, in this work, we set up two PCR reactions, TcH2AF/R and TrFR2, to distinguish T. cruzi from T. rangeli in mixed infections of vectors based on amplification of the histone H2A/SIRE and the small nucleolar RNA Cl1 genes, respectively. Both PCRs were able to appropriately detect all T. cruzi or T. rangeli experimentally infected-triatomines, as well as the S35/S36 PCR which amplifies the variable region of minicircle kDNA of T. cruzi. In mixed infections, whereas T. cruzi DNA was amplified in 100% of samples with TcH2AF/R and S35/S36 PCRs, T. rangeli was detected in 71% with TrF/R2 and in 6% with S35/S36. In a group of Rhodnius colombiensis collected from Coyaima (Colombia), T. cruzi was identified in 100% with both PCRs and T. rangeli in 14% with TrF/R2 and 10% with S35/S36 PCR. These results show that TcH2AF/R and TrF/R2 PCRs which are capable of recognizing all T. cruzi and T. rangeli strains and lineages could be useful for diagnosis as well as for epidemiological field studies of T. cruzi and T. rangeli vector infections.
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Affiliation(s)
- Paula Ximena Pavia
- Laboratorio de Parasitología Molecular, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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Souza RT, Santos MRM, Lima FM, El-Sayed NM, Myler PJ, Ruiz JC, da Silveira JF. New Trypanosoma cruzi repeated element that shows site specificity for insertion. EUKARYOTIC CELL 2007; 6:1228-38. [PMID: 17526721 PMCID: PMC1951114 DOI: 10.1128/ec.00036-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5' end of the element and a sequence domain of approximately 500 bp without a well-defined borderline at the 3' end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of approximately 0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be approximately 173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.
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Affiliation(s)
- Renata T Souza
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, UNIFESP, Rua Botucatu, São Paulo, Brazil
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Morgun A, Shulzhenko N, Perez-Diez A, Diniz RVZ, Sanson GF, Almeida DR, Matzinger P, Gerbase-DeLima M. Molecular profiling improves diagnoses of rejection and infection in transplanted organs. Circ Res 2006; 98:e74-83. [PMID: 16794196 DOI: 10.1161/01.res.0000228714.15691.8a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The monitoring of transplanted hearts is currently based on histological evaluation of endomyocardial biopsies, a method that is fairly insensitive and that does not always accurately discriminate between rejection and infection in the heart. Accurate diagnosis of rejection and infection is absolutely crucial, however, as the respective treatments are completely different. Using microarrays, we analyzed gene expression in 76 cardiac biopsies from 40 heart recipients undergoing rejection, no rejection, or Trypanosoma cruzi infection. We found a set of genes whose expression patterns were typical of acute rejection, and another set of genes that discriminated between rejection and T cruzi infection. These sets revealed acute rejection episodes up to 2 weeks earlier, and trypanosome infection up to 2 months earlier than did histological evaluation. When applied to raw data from other institutions, the 2 sets of predictive genes were also able to accurately pinpoint acute rejection of lung and kidney transplants, as well as bacterial infections in kidneys. In addition to their usefulness as diagnostic tools, the data suggest that there are similarities in the biology of the processes involved in rejection of different grafts and also in the tissue responses to pathogens as diverse as bacteria and protozoa.
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Affiliation(s)
- Andrey Morgun
- Immunogenetics Division, Pediatrics Department, Federal University of São Paulo, Brazil.
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12
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Heras SR, López MC, García-Pérez JL, Martin SL, Thomas MC. The L1Tc C-terminal domain from Trypanosoma cruzi non-long terminal repeat retrotransposon codes for a protein that bears two C2H2 zinc finger motifs and is endowed with nucleic acid chaperone activity. Mol Cell Biol 2005; 25:9209-20. [PMID: 16227574 PMCID: PMC1265797 DOI: 10.1128/mcb.25.21.9209-9220.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
L1Tc, a non-long terminal repeat retrotransposon from Trypanosoma cruzi, is a 4.9-kb actively transcribed element which contains a single open reading frame coding for the machinery necessary for its autonomous retrotransposition. In this paper, we analyze the protein encoded by the L1Tc 3' region, termed C2-L1Tc, which contains two zinc finger motifs similar to those present in the TFIIIA transcription factor family. C2-L1Tc binds nucleic acids with different affinities, such that RNA > tRNA > single-stranded DNA > double-stranded DNA, without any evidence for sequence specificity. C2-L1Tc also exhibits nucleic acid chaperone activity on different DNA templates that may participate in the mechanism of retrotransposition of the element. C2-L1Tc promotes annealing of complementary oligonucleotides, prevents melting of perfect DNA duplexes, and facilitates the strand exchange between DNAs to form the most stable duplex DNA in competitive displacement assays. Mapping of regions of C2-L1Tc using specific peptides showed that nucleic acid chaperone activity required a short basic sequence accompanied by a zinc finger motif or by another basic region such as RRR. Thus, a short basic polypeptide containing the two C(2)H(2) motifs promotes formation of the most stable duplex DNA at a concentration only three times higher than that required for C2-L1Tc.
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Affiliation(s)
- Sara R Heras
- Departamento de Biología Molecular, Instituto de Parasitología y Biomedicina López Neyra, CSIC, Avda del Conocimiento s/n, 18100 Granada, Spain
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Arkhipova IR. Mobile genetic elements and sexual reproduction. Cytogenet Genome Res 2005; 110:372-82. [PMID: 16093689 DOI: 10.1159/000084969] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Accepted: 01/02/2004] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TE) are prominent components of most eukaryotic genomes. In addition to their possible participation in the origin of sexual reproduction in eukaryotes, they may be also involved in its maintenance as important contributors to the deleterious mutation load. Comparative analyses of transposon content in the genomes of sexually reproducing and anciently asexual species may help to understand the contribution of different TE classes to the deleterious load. The apparent absence of deleterious retrotransposons from the genomes of ancient asexuals is in agreement with the hypothesis that they may play a special role in the maintenance of sexual reproduction and in early extinction for which most species are destined upon the abandonment of sex.
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Affiliation(s)
- I R Arkhipova
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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Lorenzi HA, Robledo G, Levin MJ. The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons. Mol Biochem Parasitol 2005; 145:184-94. [PMID: 16297462 DOI: 10.1016/j.molbiopara.2005.10.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 10/02/2005] [Accepted: 10/04/2005] [Indexed: 11/29/2022]
Abstract
VIPER was initially characterized as a 2326bp LTR-like retroelement associated to SIRE, a short interspersed repetitive element specific of Trypanosoma cruzi. It carried a single ORF that coded for a putative reverse transcriptase-RNAse H protein, suggesting that it could be a truncated copy of a longer retroelement. Herein we report the identification and characterization of a complete 4480bp long VIPER in the T. cruzi genome. The complete VIPER harbored three non-overlapped domains encoding for a GAG-like, a tyrosine recombinase and a reverse transcriptase-RNAse H proteins. VIPER elements were also found in the genomes of Trypanosoma brucei and Trypanosoma vivax, but not in Leishmania sp. On the basis of its reverse transcriptase phylogeny, VIPER was classified as an LTR retroelement. However, VIPER was structurally related to the tyrosine recombinase encoding retroelements, DIRS and Ngaro. Phylogenetic analysis showed that VIPER's tyrosine recombinase grouped with the transposases RCI1 of Escherichia coli and Ye24 and Ye72 of Haemophilus influenzae within a major branch of prokaryotic recombinases. Taken together, VIPER's structure, the nature of its tyrosine recombinase, the unique features of its reverse transcriptase catalytic consensus motif and the fact that it was found in Trypanosomes, an early branching eukaryote, suggest that VIPER may be the closest relative of the founder element of the tyrosine recombinase encoding retrotransposons known up to date. Our analysis revealed that tyrosine recombinase-encoding retroelements were originated as early in evolution as non-LTR retroelements and suggests that VIPER, Ngaro and DIRS elements may constitute a third group of retrotransposons, distinct from both LTR and non-LTR retroelements.
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Affiliation(s)
- Hernan A Lorenzi
- Laboratorio de Biologia Molecular de la Enfermedad de Chagas (LaBMECh) INGEBI, National Research Council (CONICET), Centro de Genomica Aplicada (CeGA), University of Buenos Aires, Vuelta de Obligado 2490 2P, 1428, Buenos Aires, Argentina
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Bringaud F, Ghedin E, Blandin G, Bartholomeu DC, Caler E, Levin MJ, Baltz T, El-Sayed NM. Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements. Mol Biochem Parasitol 2005; 145:158-70. [PMID: 16257065 DOI: 10.1016/j.molbiopara.2005.09.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 09/25/2005] [Accepted: 09/27/2005] [Indexed: 11/22/2022]
Abstract
The ingi and L1Tc non-LTR retrotransposons--which constitute the ingi clade--are abundant in the genome of the trypanosomatid species Trypanosoma brucei and Trypanosoma cruzi, respectively. The corresponding retroelements, however, are not present in the genome of a closely related trypanosomatid, Leishmania major. To study the evolution of non-LTR retrotransposons in trypanosomatids, we have analyzed all ingi/L1Tc elements and highly degenerate ingi/L1Tc-related sequences identified in the recently completed T. brucei, T. cruzi and L. major genomes. The coding sequences of 242 degenerate ingi/L1Tc-related elements (DIREs) in all three genomes were reconstituted by removing the numerous frame shifts. Three independent phylogenetic analyses conducted on the conserved domains encoded by these elements show that all DIREs, including the 52 L. major DIREs, form a monophyletic group belonging to the ingi clade. This indicates that the trypanosomatid ancestor contained active mobile elements that have been retained in the Trypanosoma species, but were lost from L. major genome, where only remnants (DIRE) are detectable. All 242 DIREs analyzed group together according to their species origin with the exception of 11 T. cruzi DIREs which are close to the T. brucei ingi/DIRE families. Considering the absence of known horizontal transfer between the African T. brucei and the South-American T. cruzi, this suggests that this group of elements evolved at a lower rate when compared to the other trypanosomatid elements. Interestingly, the only nucleotide sequence conserved between ingi and L1Tc (the first 79 residues) is also present at the 5'-extremity of all the full length DIREs and suggests a possible role for this conserved motif, as well as for DIREs.
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Affiliation(s)
- Frédéric Bringaud
- Laboratoire de Génomique Fonctionnelle Des Trypanosomatides, Université Victor Segalen Bordeaux 2, UMR-5162 CNRS, 146 Rue Léo Saignat, 33076 Bordeaux Cedex, France.
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Baptista CS, Vêncio RZN, Abdala S, Valadares MP, Martins C, de Bragança Pereira CA, Zingales B. DNA microarrays for comparative genomics and analysis of gene expression in Trypanosoma cruzi. Mol Biochem Parasitol 2005; 138:183-94. [PMID: 15555730 DOI: 10.1016/j.molbiopara.2004.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2003] [Revised: 05/25/2004] [Accepted: 06/09/2004] [Indexed: 11/27/2022]
Abstract
Trypanosoma cruzi presents high genetic diversity and parasite isolates show remarkable differences in biological parameters. In this study, we evaluated whether DNA microarrays containing CL Brener cDNAs can be used for comparative genomics and for the analysis of gene expression in T. cruzi. We constructed a prototype microarray with 710 expression sequence tags of CL Brener and 20 sequences of T. cruzi strains. These probes represent 665 unique genes. Results from four hybridisations with genomic DNA of Silvio (T. cruzi I) and CL Brener (hybrid genotype) identified 9.3% of the probes (68/730) differentially represented in the two genomes. Data from eight hybridisations with cDNA obtained from three independent parasite harvests of Silvio and CL Brener disclosed 84 sequences of 730 (11.5%) that showed statistical significant (P < or = 0.01) changes in expression (1.6-6.5-fold). Some of the array-identified sequences were confirmed by Southern and Northern blot analysis. Only 20% of the probes with increased expression in Silvio or CL Brener presented higher hybridisation with genomic DNA of either strain. Approximately 2.5% (18/730) and 9.0% (65/730) of the probes were differentially expressed (P < or = 0.01), respectively, in epimastigotes and metacyclic trypomastigotes of two T. cruzi II strains isolated from chronic chagasic patients. Microarrays identified several sequences for which differences in gene copy number and/or in the levels of RNA transcripts were previously demonstrated by different approaches. The data indicate that DNA microarrays are a useful tool for comparative studies between strains and provide further evidence for a high level of post-transcriptional regulation of RNA abundance in T. cruzi.
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Affiliation(s)
- Cassio Silva Baptista
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, CEP 05508-000 São Paulo, SP, Brazil
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17
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Ben-Dov CP, Levin MJ, Vázquez MP. Analysis of the highly efficient pre-mRNA processing region HX1 of Trypanosoma cruzi. Mol Biochem Parasitol 2005; 140:97-105. [PMID: 15694491 DOI: 10.1016/j.molbiopara.2005.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 12/31/2004] [Accepted: 01/03/2005] [Indexed: 10/25/2022]
Abstract
Gene expression in trypanosomes is controlled mainly by post-transcriptional processes. This study was designed to analyse HX1, one of the TcP2beta upstream intergenic regions. It is an efficient pre-mRNA processing region that has been widely and successfully used in Trypanosoma cruzi transfection vectors. Herein we compared its performance with other regions within the same locus, and we identified the sequence elements responsible for the HX1 efficiency in trans-splicing and protein synthesis. Our mutational analysis showed the flexibility of the branch point site selection for HX1 trans-splicing process. We demonstrated also that its 12 nt 5'UTR sequence contributes to both trans-splicing and translation efficiency. The natural insertion of the repetitive element short interspersed repetitive element (SIRE) in one of the HX1 polypyrimidine tracts decreases the translated protein level by 40%. In this report, we demonstrated that this reduction is a consequence of a decrease of five-fold in the level of processed mRNA balanced by an increased efficiency of translation due to the inclusion of a 38 nt SIRE specific sequence in the 5'UTR of the mRNA.
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Affiliation(s)
- Claudia P Ben-Dov
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, INGEBI-CONICET, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina.
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18
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Kim D, Chiurillo MA, El-Sayed N, Jones K, Santos MRM, Porcile PE, Andersson B, Myler P, da Silveira JF, Ramírez JL. Telomere and subtelomere of Trypanosoma cruzi chromosomes are enriched in (pseudo)genes of retrotransposon hot spot and trans-sialidase-like gene families: the origins of T. cruzi telomeres. Gene 2005; 346:153-61. [PMID: 15716016 DOI: 10.1016/j.gene.2004.10.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2004] [Revised: 09/06/2004] [Accepted: 10/14/2004] [Indexed: 11/23/2022]
Abstract
Here, we sequenced two large telomeric regions obtained from the pathogen protozoan Trypanosoma cruzi. These sequences, together with in silico assembled contigs, allowed us to establish the general features of telomeres and subtelomeres of this parasite. Our findings can be summarized as follows: We confirmed the presence of two types of telomeric ends; subtelomeric regions appeared to be enriched in (pseudo)genes of RHS (retrotransposon hot spot), TS (trans-sialidase)-like proteins, and putative surface protein DGF-1 (dispersed gene family-1). Sequence analysis of the ts-like genes located at the telomeres suggested that T. cruzi chromosomal ends could have been the site for generation of new gp85 variants, an important adhesin molecule involved in the invasion of mammalian cells by T. cruzi. Finally, a mechanism for generation of T. cruzi telomere by chromosome breakage and telomere healing is proposed.
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Affiliation(s)
- Dong Kim
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, UNIFESP, Rua Botucatu, 862, CEP 04023-062, S. Paulo, Brazil
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19
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Obado SO, Taylor MC, Wilkinson SR, Bromley EV, Kelly JM. Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional "strand-switch" domain as a major feature. Genome Res 2005; 15:36-43. [PMID: 15632088 PMCID: PMC540271 DOI: 10.1101/gr.2895105] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Accepted: 10/21/2004] [Indexed: 11/25/2022]
Abstract
Trypanosomatids are an ancient family that diverged from the main eukaryotic lineage early in evolution, which display several unique features of gene organization and expression. Although genome sequencing is now complete, the nature of centromeres in these and other parasitic protozoa has not been resolved. Here, we report the functional mapping of a centromere in the American trypanosome, Trypanosoma cruzi, a parasite with an unusual mechanism of genetic exchange that involves the generation of aneuploidy by nuclear hybridization. Using a telomere-associated chromosome fragmentation approach, we show that the region required for the mitotic stability of chromosome 3 encompasses a transcriptional "strand-switch" domain constituted by a 16-kb GC-rich island. The domain contains several degenerate retrotransposon-like insertions, but atypically, lacks the arrays of satellite repeats normally associated with centromeric regions. This unusual type of organization may represent a paradigm for centromeres in T. cruzi and other primitive eukaryotes.
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Affiliation(s)
- Samson O Obado
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
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20
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Goodwin TJD, Poulter RTM. A New Group of Tyrosine Recombinase-Encoding Retrotransposons. Mol Biol Evol 2004; 21:746-59. [PMID: 14963102 DOI: 10.1093/molbev/msh072] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A wide variety of novel tyrosine recombinase (YR)-encoding retrotransposons were identified using data emerging from the various eukaryotic genome sequencing projects. Although many of these elements are clearly members of the previously described DIRS group of YR retrotransposons, a substantial number, including elements from a variety of fungi and animals, belong to a distinct and previously unrecognized group. We refer to these latter elements as the Ngaro group after a representative from zebrafish. Like the members of the DIRS group, Ngaro elements encode proteins bearing reverse transcriptase (RT) and ribonuclease H (RH) domains similar to those of long terminal repeat (LTR) retrotransposons. Phylogenetic analyses based on alignments of RT/RH and YR domains, however, indicate that Ngaro and DIRS are anciently diverged groups. Differences in coding capacity also support the distinction between the two groups. For instance, we found that DIRS elements all encode a protein domain which is similar in sequence to the DNA methyltransferases of certain bacteriophages, whereas this domain is absent from all Ngaro elements. Together, the Ngaro and DIRS groups of YR retrotransposons contain elements with an astonishing diversity in structures, with variations in the nature of the associated repeat sequences and in the arrangement and complement of coding regions. In addition they contain elements with some surprising features, such as spliceosomal introns and long overlapping open reading frames.
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21
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Wickstead B, Ersfeld K, Gull K. Repetitive elements in genomes of parasitic protozoa. Microbiol Mol Biol Rev 2003; 67:360-75, table of contents. [PMID: 12966140 PMCID: PMC193867 DOI: 10.1128/mmbr.67.3.360-375.2003] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility.
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Affiliation(s)
- Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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22
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Cevallos AM, López-Villaseñor I, Espinosa N, Herrera J, Hernández R. Trypanosoma cruzi: allelic comparisons of the actin genes and analysis of their transcripts. Exp Parasitol 2003; 103:27-34. [PMID: 12810043 DOI: 10.1016/s0014-4894(03)00066-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two allelic genomic fragments containing actin genes from Trypanosoma cruzi were isolated and characterized. One allele comprises two complete tandem repeats of a sequence encoding an actin gene. In the other, only one actin gene is found. Each one of these three gene copies encode for a complete and identical potential protein of 376 amino acids which is 93% similar with its homolog from Trypanosoma brucei. Northern hybridizations of both total and polysomal RNA from epimastigotes demonstrated the presence of an actin polyadenylated mRNA of about 1.6 kb. Actin transcripts processing sites were determined by 5(')- and 3(')-RACE. The obtained sequence data demonstrates that actin genes from both alleles are expressed. The stability of actin mRNA was found to be similar to the one exhibited by the ribosomal protein S4 mRNA as an internal reference. A time course analysis of cultured epimastigotes showed a novel behaviour in which actin mRNA steady state concentration peaks during the transition from the logarithmic to the stationary phase of growth.
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MESH Headings
- Actins/chemistry
- Actins/genetics
- Alleles
- Animals
- Base Sequence
- Blotting, Northern
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Protozoan/chemistry
- Electrophoresis, Gel, Pulsed-Field
- Gene Expression
- Half-Life
- Molecular Sequence Data
- RNA Processing, Post-Transcriptional
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Protozoan/chemistry
- Sequence Alignment
- Tandem Repeat Sequences/genetics
- Trypanosoma cruzi/genetics
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Affiliation(s)
- Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70-228, CP 04510, México, D.F., Mexico
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23
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Verbisck NV, dos Santos MRM, Engman DM, Angel Chiurillo M, Ramirez JL, Araya JE, Mortara RA, da Silveira JF. A novel reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Trypanosoma cruzi. Mem Inst Oswaldo Cruz 2003; 98:129-33. [PMID: 12700870 DOI: 10.1590/s0074-02762003000100016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We report the molecular characterization of a novel reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Trypanosoma cruzi. Steady-state level of transcripts of this sequence family appeared to be developmentally regulated, since only in the replicative forms the parasite showed expression of related sequences with a major band around 3 kb. The presence of frame shifts or premature stop codons predicts that transcripts are not translated. The sequence family also contains truncated forms of retrotransposons elements that may become potential hot spots for retroelement insertion. Sequences homologous to this family are interspersed at many chromosomes including the subtelomeric regions.
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Affiliation(s)
- Newton Valério Verbisck
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, São Paulo, SP, 04023-062, Brasil
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24
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Zwir I, Zaliz RR, Ruspini EH. Automated biological sequence description by genetic multiobjective generalized clustering. Ann N Y Acad Sci 2002; 980:65-82. [PMID: 12594082 DOI: 10.1111/j.1749-6632.2002.tb04889.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in the accessibility of databases containing representations of complex objects-exemplified by repositories of time-series data, information about biological macromolecules, or knowledge about metabolic pathways-have not been matched by availability of tools that facilitate the retrieval of objects of particular interest and aid understanding their structure and relations. In applications, such as the analysis of DNA sequences, on the other hand, requirements to retrieve objects on the basis of qualitative characteristics are poorly met by descriptions that emphasize precision and detail rather than structural features. This paper presents a method for identification of interesting qualitative features in biological sequences. Our approach relies on a generalized clustering methodology in which the features being sought correspond to the solutions of a multivariable, multiobjective optimization problem with features generally corresponding to fuzzy subsets of the object being represented. Foremost among the optimization objectives being considered are measures of the degree by which features resemble prototypical structures deemed to be interesting by database users. Other objectives include feature size and, in some cases, performance criteria related to domain-specific constraints. Genetic-algorithm methods are employed to solve the multiobjective optimization problem. These optimization algorithms discover candidate features as subsets of the object being described and that lie in the set of all Pareto-optimal solutions-of that problem. These candidate features are then summarized, employing again evolutionary-computation methods, and interrelated by employing domain-specific relations of interest to the end users. We present results of the application of this two-step method to the recognition and summarization of interesting features in DNA sequences of Tripanosoma cruzi.
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Affiliation(s)
- I Zwir
- Department of Molecular Microbiology, Howard Hughes Medical Institute Research Laboratories, Washington University School of Medicine, Saint Louis, Missouri 63110-1093, USA.
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25
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Willhoeft U, Buss H, Tannich E. The abundant polyadenylated transcript 2 DNA sequence of the pathogenic protozoan parasite Entamoeba histolytica represents a nonautonomous non-long-terminal-repeat retrotransposon-like element which is absent in the closely related nonpathogenic species Entamoeba dispar. Infect Immun 2002; 70:6798-804. [PMID: 12438355 PMCID: PMC133045 DOI: 10.1128/iai.70.12.6798-6804.2002] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While comparing gene expression in the pathogenic organism Entamoeba histolytica and the closely related but nonpathogenic species Entamoeba dispar, we discovered that the E. histolytica abundant polyadenylated transcript 2 (ehapt2) and corresponding genomic copies are absent in E. dispar. Although polyadenylated, ehapt2 does not contain any overt open reading frame. Southern blot and sequence analyses revealed that about 500 copies of ehapt2 genomic elements were present in each cell and that the copies were distributed throughout the ameba genome. The various ehapt2 elements are regularly located in the vicinity of protein-encoding genes, downstream of pyrimidine-rich sequence stretches (40 to 125 bp; CT content, 79.2 to 85.5%), and are flanked by duplicated target sites of variable length. Target site duplications were obviously generated during integration of ehapt2 into the E. histolytica genome as one copy of the flanking repeat and the complete ehapt2 element are specifically absent in orthologous E. dispar genomic sequences. ehapt2 shares 3' sequences with EhRLE, a recently identified non-long-terminal-repeat (non-LTR) retrotransposon-like element of E. histolytica, which contains a conceptual open reading frame for reverse transcriptase. Thus, ehapt2 has all of the properties of nonautonomous non-LTR retrotransposons. A comparison of various E. histolytica isolates suggested that transposition of ehapt2 takes place at a very low frequency as the genomic localization of ehapt2 elements was found to be well conserved. A mobile element such as ehapt2 could be a suitable mechanism to explain the infrequent and late transition of E. histolytica from a harmless gut commensal to an invasive pathogen.
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Affiliation(s)
- Ute Willhoeft
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
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26
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Abstract
Mobile genetic elements, by virtue of their ability to move to new chromosomal locations, are considered important in shaping the evolutionary course of the genome. They are widespread in the biological kingdom. Among the protozoan parasites several types of transposable elements are encountered. The largest variety is seen in the trypanosomatids-Trypanosoma brucei, Trypanosoma cruzi and Crithidia fasciculata. They contain elements that insert site-specifically in the spliced-leader RNA genes, and others that are dispersed in a variety of genomic locations. Giardia lamblia contains three families of transposable elements. Two of these are subtleomeric in location while one is chromosome-internal. Entamoeba histolytica has an abundant retrotransposon dispersed in the genome. Nucleotide sequence analysis of all the elements shows that they are all retrotransposons, and, with the exception of one class of elements in T. cruzi, all of them are non-long-terminal-repeat retrotransposons. Although most copies have accumulated mutations, they can potentially encode reverse transcriptase, endonuclease and nucleic-acid-binding activities. Functionally and phylogenetically they do not belong to a single lineage, showing that retrotransposons were acquired early in the evolution of protozoan parasites. Many of the potentially autonomous elements that encode their own transposition functions have nonautonomous counterparts that probably utilize the functions in trans. In this respect these elements are similar to the mammalian LINEs and SINEs (long and short interspersed DNA elements), showing a common theme in the evolution of retrotransposons. So far there is no report of a DNA transposon in any protozoan parasite. The genome projects that are under way for most of these organisms will help understand the evolution and possible function of these genetic elements.
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Affiliation(s)
- Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.
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27
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Chiurillo MA, Santos MRM, Franco Da Silveira J, Ramírez JL. An improved general approach for cloning and characterizing telomeres: the protozoan parasite Trypanosoma cruzi as model organism. Gene 2002; 294:197-204. [PMID: 12234681 DOI: 10.1016/s0378-1119(02)00768-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We here describe a general strategy for cloning and characterizing telomeric and sub-telomeric regions of the human protozoan parasite Trypanosoma cruzi. The use of a bacterial artificial chromosome vector and a telomeric adaptor produced stable telomeric recombinant clones with inserts ranging from 5 to 25 kb. Analysis of these recombinants provided unique landmarks for chromosomal mapping and sequencing and enabled us to derive a more accurate picture of T. cruzi telomeric organization.
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Affiliation(s)
- Miguel Angel Chiurillo
- Laboratorio de Genetica Molecular, Instituto de Biologia Experimental Universidad Central de Venezuela calle Suapure, Colinas de Bello Monte, Apdo 47525, Caracas 1041-A, Venezuela
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28
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Lorenzi HA, Vázquez MP, Levin MJ. The genes for a DEAH RNA helicase, a NifU like protein and the translation factor eIF6 constitute the SZ5 locus of Trypanosoma cruzi. Mol Biochem Parasitol 2000; 111:207-11. [PMID: 11087930 DOI: 10.1016/s0166-6851(00)00297-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- H A Lorenzi
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI)-CONICET, University of Buenos Aires, Vuelta de Obligado 2490, 2P., 1428, Buenos Aires, Argentina
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