Guide RNAs of the recently isolated LEM125 strain of Leishmania tarentolae: An unexpected complexity

Gao, Ge; Kapushoc, Stephen T.; Simpson, Agda M.; Thiemann, Otávio Henrique; Simpson, Larry

doi:10.1017/s1355838201018076

Cited by 27 publications

(32 citation statements)

References 34 publications

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“…Remarkably, short stretches from frames 1 and 3 yielded significant sequence homology with the Q7M3U1 entry, which corresponds to the NADH dehydrogenase subunit 8 (ND8,G1) of L. tarentolae. In this species, the protein is encoded by the G1 cryptogene that needs to be extensively edited to yield a translatable mRNA (Gao et al 2001;Thiemann et al 1994). Similarly, in T. brucei, the homologous cryptogene, named CR1, is edited by the addition of 259 uridines and the removal of 46 uridines (Souza et al 1992).…”

Section: Resultsmentioning

confidence: 99%

“…Figure 2 shows the alignment of ND8 cryptogenes from these four Leishmania species, evidencing remarkable sequence conservation, which suggests both a selective pressure to maintain the DNA sequence and, probably, a functional importance for these cryptogenes. This high sequence conservation prompted us to deduce a theoretical edited transcript for L. braziliensis ND8 based on the edited ND8 transcript sequence in L. tarentolae (Gao et al 2001). As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Genomically encoded nucleotides are shown in upper case, inserted uridines with lower case (u), and deleted residues are indicated with asterisks. Experimentally deduced editing events, according to the 600D cDNA, are shaded in green, whereas those inferred by sequence comparison with LtND8 transcript (Gao et al 2001;Thiemann et al 1994) are shaded in yellow. Gaps (shown with dashes) were introduced to maximize alignment.…”

Section: Resultsmentioning

confidence: 99%

“…4). The complete edition of G1 transcript in L. tarentolae requires the sequential use of 13 gRNAs (Gao et al 2001;Thiemann et al 1994). The edition of the partially edited ND8 in the 600D cDNA would need of the use of gRNAs equivalent to L. tarentolae gND8-I, -II, -III, and -IV RNA guides.…”

Section: Resultsmentioning

confidence: 99%

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Evidence of RNA editing in Leishmania braziliensis promastigotes

2010

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RNA editing in trypanosomatids is an elaborate form of post-transcriptional processing that inserts and deletes uridines in many mitochondrial pre-mRNAs, providing the genetic information needed to create functional transcripts. The process has been extensively analyzed in Trypanosoma brucei, Crithidia fasciculata, and Leishmania tarentolae. However, few data exist on this mechanism in pathogenic Leishmania species. Here, we show evidence that this process also operates in Leishmania braziliensis, being the first time that RNA editing has been described in a species of the Viannia subgenus. A partially edited transcript corresponding to the NADH dehydrogenase subunit 8 (ND8) gene was identified in L. braziliensis promastigotes. Sequence analysis allowed the identification of the maxicircle-encoded cryptogene, which shows a high degree of sequence conservation with the corresponding cryptogenes in other Leishmania species. Although an edition pattern could be postulated for the ND8 transcripts in L. braziliensis, attempts to isolate completely edited transcripts by RT-PCR were not fruitful; instead, many transcripts with partial and unexpected editing patterns were isolated. This data, together with our inability to detect full-size transcripts by Northern blotting in promastigotes of L. braziliensis, led us to the suggestion that the strain used in this study (M2904) lacks of critical RNA guides for a complete edition of ND8 transcripts.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Evidence of RNA editing in Leishmania braziliensis promastigotes

2010

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“…While some gRNAs exhibit single or more mismatches to their cognate mRNA targets 6,13,14,20,21 other gRNAs are characterized by extensive mismatches, thus bringing into question whether they are able to direct proper editing. 22 However, gRNAs that have retained a perfect anchor sequence but exhibit mismatches within the guiding domain might actually direct alternative editing reactions. In T. brucei and Leishmania tarentolae, mRNAs exhibiting alternative editing events have been reported for several genes (e.g., CO3, RPS12 or ND3) [23][24][25] but have been interpreted as misediting products.…”

Section: Research Papermentioning

confidence: 99%

Identification of novel guide RNAs from the mitochondria ofTrypanosoma brucei

Madej¹,

Niemann²,

Hüttenhofer³

et al. 2008

RNA Biology

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The majority of mitochondrial mRNAs in African trypanosomes are subject to an RNA editing reaction, which is characterized by the insertion and/or deletion of U nucleotides only. The reaction creates functional mRNAs and is catalyzed by a high molecular mass enzyme complex, the editosome. Editosomes interact with a unique class of small non-coding, 3'-oligouridylated (oU) RNAs, so-called guide RNAs (gRNAs). Guide RNAs function as transacting templates in the U deletion/insertion reaction and thus, represent key components in the reaction cycle. Furthermore, by utilizing different gRNAs, alternative editing events can take place, thereby expanding the protein diversity in the mitochondria of the parasites. In this study, we have analyzed small, non-coding mitochondrial transcripts from Trypanosoma brucei. By generating cDNA libraries from size-selected RNA populations we identified 51 novel oU-RNAs. For 29 of these RNAs we were able to predict cognate mRNA targets. By Northern blot analysis, we verified the expression of 22 of these oU-RNAs and demonstrate that they share all known gRNA characteristics. Five of these 51 putative gRNAs are characterized by single mismatches to their cognate, fully edited mRNA sequences suggesting that they could act as gRNAs for alternative editing events.

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High throughput sequencing revolution reveals conserved fundamentals of U‐indel editing

2018

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Among Euglenozoans, mitochondrial RNA editing occurs in the diplonemids and in the kinetoplastids that include parasitic trypanosomes. Yet U-indel editing, in which open reading frames (ORFs) on mRNAs are generated by insertion and deletion of uridylates in locations dictated by guide RNAs, appears confined to kinetoplastids. The nature of guide RNA and edited mRNA populations has been cursorily explored in a surprisingly extensive number of species over the years, although complete sets of fully edited mRNAs for most kinetoplast genomes are largely missing. Now, however, high throughput sequencing technologies have had an enormous impact on what we know and will learn about the mechanisms, benefits, and final edited products of U-indel editing. Tools including PARERS, TREAT, and T-Aligner function to organize and make sense of U-indel mRNA transcriptomes, which are comprised of mRNAs harboring uridylate indels both consistent and inconsistent with translatable products. From high throughput sequencing data come arguments that partially edited mRNAs containing "junction regions" of noncanonical editing are editing intermediates, and conversely, arguments that they are dead-end products. These data have also revealed that the percent of a given transcript population that is fully or partially edited varies dramatically between transcripts and organisms. Outstanding questions that are being addressed include the prevalence of sequences that apparently encode alternative ORFs, diversity of editing events in ORF termini and 5' and 3' untranslated regions, and the differences that exist in this byzantine process between species. High throughput sequencing technologies will also undoubtedly be harnessed to probe U-indel editing's evolutionary origins. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Evolution and Genomics > Computational Analyses of RNA.

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Guide RNAs of the recently isolated LEM125 strain of Leishmania tarentolae: An unexpected complexity

Cited by 27 publications

References 34 publications

Evidence of RNA editing in Leishmania braziliensis promastigotes

Evidence of RNA editing in Leishmania braziliensis promastigotes

Identification of novel guide RNAs from the mitochondria ofTrypanosoma brucei

High throughput sequencing revolution reveals conserved fundamentals of U‐indel editing

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