Diversity and Evolution of Mitochondrial RNA Editing Systems

Gray, Michael W.

doi:10.1080/1521654031000119425

Cited by 90 publications

(86 citation statements)

References 45 publications

(57 reference statements)

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“…There are many more complexities regarding how various DNA elements code for a product, such as RNA editing and translational recoding (Gray 2003;Baranov et al 2003), overlapping genes (Mottus et al 1997), transcription in different reading frames (Sharpless and DePinho 1999), and antisense transcription (Dorn and Krauss 2003;Yelin et al 2003).…”

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confidence: 99%

The epistemic goal of a concept: accounting for the rationality of semantic change and variation

Brigandt

2009

Synthese

112

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Abstract:The discussion presents a framework of concepts that is intended to account for the rationality of semantic change and variation, suggesting that each scientific concept consists of three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these components, and that change in the concept's inferential role and reference can be accounted for as being rational relative to the third component, the concept's epistemic goal. This framework is illustrated and defended by application to the history of the gene concept. It is explained how the molecular gene concept grew rationally out of the classical gene concept despite a change in reference, and why the use and reference of the contemporary molecular gene concept may legitimately vary from context to context. This essay presents a framework of concepts that is designed to account for the rationality of semantic change. Though many previous discussions of conceptual change have emphasized the notion of reference, I argue that an adequate account has to acknowledge several semantic properties. More precisely, I suggest that each theoretical concept consists of three THE EPISTEMIC GOAL OF A CONCEPT 2 components of content: 1) the concept's reference, 2) its inferential role, and 3) the epistemic goal pursued by the concept's use. While reference and inferential role have been recognized by previous theories of concepts, I introduce the epistemic goal pursued by a term's use as a genuine semantic property of a term as it accounts for the rationality of semantic change and variation, in particular change in a term's inferential role and reference.After the presentation of this framework and how it is intended to account for semantic change in Section 1, the remainder of the paper defends and illustrates the framework by application to a concrete case from biology: the change of the gene concept. The first part of this case study (Section 2) discusses how the molecular gene concept grew out of the classical gene concept. While the transition from classical to molecular genetics has been subject to extensive discussion, previous accounts have been less explicit about the rationality of the semantic change that occurred with the advent of the molecular gene concept. I explain why

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confidence: 99%

The epistemic goal of a concept: accounting for the rationality of semantic change and variation

Brigandt

2009

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112

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“…Yet the majority of extant eukaryotic diversity is constituted by protists 10 , of which only a very small fraction has their mtDNA characterized. Still, the available mt genomes of protists show a range of bizarre gene arrangements, modes of organization, and complex post-transcriptional maturations 11, 12 . Hence, it does not come as a surprise that some authors consider further sequencing of mt genomes of metazoans as superfluous and non-informative but that at the same time they call for focusing efforts onto the organellar genomes of hitherto-neglected protist groups 12 .…”

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confidence: 99%

From simple to supercomplex: mitochondrial genomes of euglenozoan protists

et al. 2016

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Mitochondria are double membrane organelles of endosymbiotic origin, best known for constituting the centre of energetics of a eukaryotic cell. They contain their own mitochondrial genome, which as a consequence of gradual reduction during evolution typically contains less than two dozens of genes. In this review, we highlight the extremely diverse architecture of mitochondrial genomes and mechanisms of gene expression between the three sister groups constituting the phylum Euglenozoa - Euglenida, Diplonemea and Kinetoplastea. The earliest diverging euglenids possess a simplified mitochondrial genome and a conventional gene expression, whereas both are highly complex in the two other groups. The expression of their mitochondrial-encoded proteins requires extensive post-transcriptional modifications guided by complex protein machineries and multiple small RNA molecules. Moreover, the least studied diplonemids, which have been recently discovered as a highly abundant component of the world ocean plankton, possess one of the most complicated mitochondrial genome organisations known to date.

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“…35). 2 An intriguing possibility is that this activity is derived from phylogenetically widespread but poorly characterized enzymes that are responsible for the maintenance of tRNA 5Ј-ends, much as the ATP(CTP):tRNA nucleotidyltransferase adds and maintains the 3Ј -CCA OH tail across the three domains of life. An activity of this sort would remain relatively cryptic in genomic and in vitro studies, as it would act only on 5Ј-degraded tRNAs to regenerate proper acceptor stem base pairing.…”

Section: An In Vitro Assay Of Mitochondrial Trna Editing In S Punctamentioning

confidence: 99%

“…The term "RNA editing" was coined to describe post-transcriptional U insertions within the mitochondrial cox2 transcript of two trypanosome species: insertions that correct a gene-predicted frameshift, thereby generating a functional mRNA (1). Editing has since been found to be an essential process in many diverse, predominantly organellar, systems (2). Many cases of mRNA editing have been identified, including uridylate insertion/deletion in trypanosome mitochondria (3,4), co-transcriptional insertion of nucleotides in myxomycete mitochondria (5,6), C-to-U and U-to-C editing in plant mitochondria and chloroplasts (7), Ato-I (8, 9) and C-to-U (10) base deamination in animal nuclei, co-transcriptional nucleotide insertion in viruses (11), and the recently discovered nucleotide replacement editing in dinoflagellate mitochondria (12).…”

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confidence: 99%

In Vitro Characterization of a tRNA Editing Activity in the Mitochondria of Spizellomyces punctatus, a Chytridiomycete Fungus

Bullerwell

Gray

2005

Journal of Biological Chemistry

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In the chytridiomycete fungus, Spizellomyces punctatus, all eight of the mitochondrially encoded tRNAs are predicted to have one or more base pair mismatches at the first three positions of their aminoacyl acceptor stems. These tRNAs are edited post-transcriptionally by replacement of the 5-nucleotide in each mismatched pair with a nucleotide that can form a standard Watson-Crick base pair with its counterpart in the 3-half of the stem. The type of mitochondrial tRNA editing found in S. punctatus also occurs in Acanthamoeba castellanii, a distantly related amoeboid protist. Using an S. punctatus mitochondrial extract, we have developed an in vitro assay of tRNA editing in which nucleotides are incorporated into various tRNA substrates. Experiments employing synthetic transcripts revealed that the S. punctatus tRNA editing activity incorporates nucleotides on the 5-side of substrate tRNAs, uses the 3-sequence as a template for incorporation, and adds nucleotides in a 3-to-5 direction. This activity can add nucleotides to a triphosphorylated 5-end in the absence of ATP but requires ATP to add nucleotides to a monophosphorylated 5-end; moreover, it functions independently of the state of tRNA 3 processing. These data parallel results obtained in a previous in vitro study of A. castellanii tRNA editing, suggesting that remarkably similar activities function in the mitochondria of these two organisms. The evolutionary origins of these activities are discussed.

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Diversity and Evolution of Mitochondrial RNA Editing Systems

Cited by 90 publications

References 45 publications

The epistemic goal of a concept: accounting for the rationality of semantic change and variation

The epistemic goal of a concept: accounting for the rationality of semantic change and variation

From simple to supercomplex: mitochondrial genomes of euglenozoan protists

In Vitro Characterization of a tRNA Editing Activity in the Mitochondria of Spizellomyces punctatus, a Chytridiomycete Fungus

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