Trypanosome <scp>RNA</scp> editing: the complexity of getting U in and taking U out

Read, Laurie K.; Lukeš, Julius; Hashimi, Hassan

doi:10.1002/wrna.1313

Cited by 130 publications

(176 citation statements)

References 85 publications

(381 reference statements)

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“…These organisms share unique biology, including the essential process termed mitochondrial uridine (U) insertion/deletion RNA editing (Aphasizhev and Aphasizheva 2011b;Hashimi et al 2013;Read et al 2016). Kinetoplastids are characterized by their unusual mitochondrial DNA structure, the kinetoplast, or kDNA.…”

Section: Introductionmentioning

confidence: 99%

“…Twelve of the 18 protein coding genes encoded in the maxicircles are referred to as cryptogenes because they do not encode functional open reading frames. Prior to translation, these mRNAs must be altered by the specific addition and less frequent deletion of U's by RNA editing (Aphasizhev and Aphasizheva 2011b;Hashimi et al 2013;Read et al 2016). The precise insertion and deletion of U residues is guided by small, noncoding guide RNAs (gRNAs), which act as templates.…”

Section: Introductionmentioning

confidence: 99%

“…gRNAs are encoded almost exclusively in the minicircle component of kDNA. The enzymes that catalyze U insertion/deletion during kinetoplastid RNA editing are part of a multiprotein complex termed the RNA editing core complex (RECC) or 20S editosome (Rusche et al 1997(Rusche et al , 2001Cruz-Reyes et al 2002;Aphasizhev et al 2003;Ernst et al 2003;Panigrahi et al 2003Panigrahi et al , 2006Stuart et al 2005;Trotter et al 2005;Carnes et al 2008Carnes et al , 2011Read et al 2016). Distinct RECC variants catalyze U insertion and U deletion, although it is not known whether these are stable complexes, or whether proteins specific for insertion or deletion shuttle on and off a common base of proteins (Carnes et al 2008(Carnes et al , 2011.…”

Section: Introductionmentioning

confidence: 99%

“…Though RECC is necessary for the editing process, it is not sufficient. Numerous recent studies have demonstrated that a large, possibly dynamic and heterogeneous complex termed MRB1 (mitochondrial RNA binding complex 1) or RESC (RNA editing substrate binding complex) is also essential for RNA editing in kinetoplastids (Fisk et al 2008;Hashimi et al 2008Hashimi et al , 2009Hashimi et al , 2013Weng et al 2008;Acestor et al 2009;Ammerman et al 2011Ammerman et al , 2012Ammerman et al , 2013Kafkova et al 2012;Aphasizheva et al 2014;Huang et al 2015;Madina et al 2015;Read et al 2016). Indeed, the MRB1 complex likely acts as the platform for RNA editing, since it contains readily detectable mRNA and gRNA, while purified RECC lacks associated RNA (Weng et al 2008;Aphasizheva et al 2014;Madina et al 2014Madina et al , 2015.…”

Section: Introductionmentioning

confidence: 99%

“…Indeed, the MRB1 complex likely acts as the platform for RNA editing, since it contains readily detectable mRNA and gRNA, while purified RECC lacks associated RNA (Weng et al 2008;Aphasizheva et al 2014;Madina et al 2014Madina et al , 2015. MRB1 appears to be composed of interacting subcomplexes with distinct roles in the editing process, and it transiently associates with other proteins that impact mitochondrial RNA editing and processing (Hashimi et al 2008(Hashimi et al , 2009Weng et al 2008;Ammerman et al 2011Ammerman et al , 2012Kafkova et al 2012;Aphasizheva et al 2014;Madina et al 2014Madina et al , 2015Read et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing

Simpson

Bruno

Bard

et al. 2016

RNA

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145

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Uridine insertion/deletion RNA editing in kinetoplastids entails the addition and deletion of uridine residues throughout the length of mitochondrial transcripts to generate translatable mRNAs. This complex process requires the coordinated use of several multiprotein complexes as well as the sequential use of noncoding template RNAs called guide RNAs. The majority of steadystate mitochondrial mRNAs are partially edited and often contain regions of mis-editing, termed junctions, whose role is unclear. Here, we report a novel method for sequencing entire populations of pre-edited partially edited, and fully edited RNAs and analyzing editing characteristics across populations using a new bioinformatics tool, the Trypanosome RNA Editing Alignment Tool (TREAT). Using TREAT, we examined populations of two transcripts, RPS12 and ND7-5 ′ , in wild-type Trypanosoma brucei. We provide evidence that the majority of partially edited sequences contain junctions, that intrinsic pause sites arise during the progression of editing, and that the mechanisms that mediate pausing in the generation of canonical fully edited sequences are distinct from those that mediate the ends of junction regions. Furthermore, we identify alternatively edited sequences that constitute plausible alternative open reading frames and identify substantial variability in the 5 ′ UTRs of both canonical and alternatively edited sequences. This work is the first to use high-throughput sequencing to examine full-length sequences of whole populations of partially edited transcripts. Our method is highly applicable to current questions in the RNA editing field, including defining mechanisms of action for editing factors and identifying potential alternatively edited sequences.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing

Simpson

Bruno

Bard

et al. 2016

RNA

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145

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Massive mitochondrial DNA content in diplonemid and kinetoplastid protists

et al. 2018

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SummaryThe mitochondrial DNA of diplonemid and kinetoplastid protists is known for its suite of bizarre features, including the presence of concatenated circular molecules, extensive trans‐splicing and various forms of RNA editing. Here we report on the existence of another remarkable characteristic: hyper‐inflated DNA content. We estimated the total amount of mitochondrial DNA in four kinetoplastid species (Trypanosoma brucei, Trypanoplasma borreli, Cryptobia helicis, and Perkinsela sp.) and the diplonemid Diplonema papillatum. Staining with 4′,6‐diamidino‐2‐phenylindole and RedDot1 followed by color deconvolution and quantification revealed massive inflation in the total amount of DNA in their organelles. This was further confirmed by electron microscopy. The most extreme case is the ∼260 Mbp of DNA in the mitochondrion of Diplonema, which greatly exceeds that in its nucleus; this is, to our knowledge, the largest amount of DNA described in any organelle. Perkinsela sp. has a total mitochondrial DNA content ~6.6× greater than its nuclear genome. This mass of DNA occupies most of the volume of the Perkinsela cell, despite the fact that it contains only six protein‐coding genes. Why so much DNA? We propose that these bloated mitochondrial DNAs accumulated by a ratchet‐like process. Despite their excessive nature, the synthesis and maintenance of these mtDNAs must incur a relatively low cost, considering that diplonemids are one of the most ubiquitous and speciose protist groups in the ocean. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology., 70(12):1267–1274, 2018

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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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Trypanosome RNA editing: the complexity of getting U in and taking U out

Cited by 130 publications

References 85 publications

High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing

High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing

Massive mitochondrial DNA content in diplonemid and kinetoplastid protists

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

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