Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites

Padilla-Mejía, Norma E.; Florencio-Martínez, Luis E.; Figueroa-Angulo, Elisa E.; Manning‐Cela, Rebeca; Hernández‐Rivas, Rosaura; Myler, Peter J.; Martínez‐Calvillo, Santiago

doi:10.1186/1471-2164-10-232

Cited by 33 publications

(53 citation statements)

References 44 publications

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“…Despite these differences in tRNA Tyr copy number, intron length, and sequence content, the mature tRNA Tyr is still highly conserved and has identical sequences in the different trypanosomatids (Padilla-Mejía et al 2009). However, because in all eukaryotes the trypanosomatid tRNA introns interrupt the anticodon loop, splicing is still an essential step in maturation and generation of a fully functional tRNA Tyr .…”

Section: Introductionmentioning

confidence: 99%

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNA^Tyr

Lopes

Silveira

Eitler

et al. 2016

RNA

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Trypanosoma brucei, the etiologic agent of sleeping sickness, encodes a single intron-containing tRNA, tRNA Tyr , and splicing is essential for its viability. In Archaea and Eukarya, tRNA splicing requires a series of enzymatic steps that begin with intron cleavage by a tRNA-splicing endonuclease and culminates with joining the resulting tRNA exons by a splicing tRNA ligase.Here we explored the function of TbTrl1, the T. brucei homolog of the yeast Trl1 tRNA ligase. We used a combination of RNA interference and molecular biology approaches to show that down-regulation of TbTrl1 expression leads to accumulation of intron-containing tRNA Tyr and a concomitant growth arrest at the G1 phase. These defects were efficiently rescued by expression of an "intronless" version of tRNA Tyr in the same RNAi cell line. Taken together, these experiments highlight the crucial importance of the TbTrl1 for tRNA Tyr maturation and viability, while revealing tRNA splicing as its only essential function.

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Section: Introductionmentioning

confidence: 99%

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNA^Tyr

Lopes

Silveira

Eitler

et al. 2016

RNA

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“…Analysis of the promoter sequences from tRNA-Sec genes in trypanosomatids indicated that box A contains an additional A residue between bases 2 and 3 (TGAGCTCAGCTGG, in which the additional A residue is underlined) compared with the consensus sequence (TGGCTCAGCTGG) (21). A similar insertion was previously reported in tRNA-Sec genes from other organisms (30).…”

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confidence: 62%

“…In Leishmania major, most tRNA genes are organized into clusters of 2 to 10 genes that may contain other Pol III-transcribed genes, and the majority of the clusters are located at the boundaries of PGCs (20,21). However, some tRNA genes are single genes that are not part of a cluster, and some of them are located inside PGCs.…”

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confidence: 99%

“…The consensus sequences of trypanosomatid tRNA promoter elements were determined by analyzing the sequences of all tRNA genes in L. major, T. brucei, and T. cruzi and comparing them to the sequences of boxes A and B from Saccharomyces cerevisiae (21,29). Analysis of the promoter sequences from tRNA-Sec genes in trypanosomatids indicated that box A contains an additional A residue between bases 2 and 3 (TGAGCTCAGCTGG, in which the additional A residue is underlined) compared with the consensus sequence (TGGCTCAGCTGG) (21).…”

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confidence: 99%

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The Selenocysteine tRNA Gene in Leishmania major Is Transcribed by both RNA Polymerase II and RNA Polymerase III

et al. 2015

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dEukaryotic tRNAs, transcribed by RNA polymerase III (Pol III), contain boxes A and B as internal promoter elements. One exception is the selenocysteine (Sec) tRNA (tRNA-Sec), whose transcription is directed by an internal box B and three extragenic sequences in vertebrates. Here we report on the transcriptional analysis of the tRNA-Sec gene in the protozoan parasite Leishmania major. This organism has unusual mechanisms of gene expression, including Pol II polycistronic transcription and maturation of mRNAs by trans splicing, a process that attaches a 39-nucleotide miniexon to the 5= end of all the mRNAs. In L. major, tRNA-Sec is encoded by a single gene inserted into a Pol II polycistronic unit, in contrast to most tRNAs, which are clustered at the boundaries of polycistronic units. 5= rapid amplification of cDNA ends and reverse transcription-PCR experiments showed that some tRNA-Sec transcripts contain the miniexon at the 5= end and a poly(A) tail at the 3= end, indicating that the tRNA-Sec gene is polycistronically transcribed by Pol II and processed by trans splicing and polyadenylation, as was recently reported for the tRNA-Sec genes in the related parasite Trypanosoma brucei. However, nuclear run-on assays with RNA polymerase inhibitors and with cells that were previously UV irradiated showed that the tRNA-Sec gene in L. major is also transcribed by Pol III. Thus, our results indicate that RNA polymerase specificity in Leishmania is not absolute in vivo, as has recently been found in other eukaryotes.

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“…Some of the differences between isodecoder genes occur in the internal promoter elements suggesting that the expression of some isoacceptor tRNA genes in Tritryps is differentially controlled [36].…”

Section: Publication Of the Three Tritryp Genomes (T Cruzi Tmentioning

confidence: 99%

Functional Genomics and Insights into Trypanosoma cruzi Gene Expression Regulation

Ávila

Goldenberg

2010

TOPARAJ

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Abstract:The regulation of gene expression in trypanosomatids is predominantly post-transcriptional. Polycistronic transcripts are processed by the addition of a common 5'-spliced leader and polyadenylation. However, the processed mRNAs are not necessarily functionally related, suggesting the existence of mechanisms for the degradation or storage of untranslatable mRNAs. Determination of the TriTryps (Leishmania major, Trypanosoma brucei and Trypanosoma cruzi) genome sequences has allowed the identification of genes encoding potential regulatory proteins. This review discusses some of the mechanisms and regulatory elements involved in cytoplasmic gene expression regulation in Trypanosoma cruzi. We also discuss how functional genomic tools have contributed toward determining the role played by RNA binding protein complexes, supporting the concept of "post-transcriptional RNA operons" or "RNA regulons". This suggests the existence of interconnected regulatory networks in the parasite, in which RNA granules act as protagonists in cytoplasmic mRNA metabolism.Keywords: Trypanosoma cruzi, RNA binding protein, gene expression regulation, functional genomics. TRANSCRIPTION OF MESSENGER RNATrypanosoma cruzi (T. cruzi) is the protozoan parasite causing Chagas disease, a major disease endemic to Latin America. It belongs to the Kinetoplastida order and has a complex life cycle, alternating between insect vectors and mammalian hosts. In both hosts, T. cruzi goes through morphological and functional changes, creating non-infective and infective forms. Those changes resulted from selective adaptation and are the major consequence of differential gene expression. Being a single cell, it needs to quickly regulate the synthesis of several proteins for rapid adaptation to a different environment. Its protein synthesis has particular characteristics in comparison with higher eukaryotes. For example, the protein-coding genes are organized into polycistronic transcription units; however, in contrast to what occurs in bacterial operons, the polycistronic units must be transcriptionally processed together before translation. In this case, polycistronic RNAs are converted into monocistronic messenger RNAs (mRNAs) through two coupled events: trans-splicing and polyadenylation. During transsplicing, a 39-nt spliced leader (SL) RNA molecule is joined to the 5' terminus of the mature transcript, while a poly(A) tail is polymerized at the 3' terminus. The same polycistronic RNA can contain functionally unrelated genes, which yield very different steady-state mRNA levels and/or which are differentially expressed during the life cycle [see review inAnother trypanosome transcription characteristic is the absence of defined RNA polymerase II (pol II) promoters. There are a few exceptions, however, such as the genes *Address correspondence to these authors at the Instituto Carlos Chagas -ICC, Fiocruz-Paraná, Rua Prof. Algacyr Munhoz Madder 3775, Curitiba, PR. Brazil; Tel: +55-41-33163230; Fax: +55-41-33163267; E-mails: sgoldenb@fiocruz.br, aravi...

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Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites

Cited by 33 publications

References 44 publications

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNA^Tyr

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNA^Tyr

The Selenocysteine tRNA Gene in Leishmania major Is Transcribed by both RNA Polymerase II and RNA Polymerase III

Functional Genomics and Insights into Trypanosoma cruzi Gene Expression Regulation

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Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites

Cited by 33 publications

References 44 publications

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNATyr

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNATyr

The Selenocysteine tRNA Gene in Leishmania major Is Transcribed by both RNA Polymerase II and RNA Polymerase III

Functional Genomics and Insights into Trypanosoma cruzi Gene Expression Regulation

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The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNA^Tyr

The essential function of the Trypanosoma brucei Trl1 homolog in procyclic cells is maturation of the intron-containing tRNA^Tyr