RNA editing in plant mitochondria: 20 years later

Gray, Michael W.

doi:10.1002/iub.272

Cited by 21 publications

(16 citation statements)

References 41 publications

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“…Recent evidence indicates that a particular class of pentatricopeptide repeat proteins (PPR) is involved in a number of processes within plant mitochondria, and that their proliferation roughly corresponds with the number of edited sites present in different lineages [[42] and references therein]. Hence, an increased understanding of the role of PPR proteins may hold the key to a better understanding of the evolution of RNA editing in plant mitochondria.…”

Section: Resultsmentioning

confidence: 99%

Are substitution rates and RNA editing correlated?

et al. 2010

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BackgroundRNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are found in some groups. The underlying processes responsible for the distribution of edited sites are largely unknown, but gene function, substitution rate, and gene conversion have been proposed to influence editing frequencies.ResultsWe studied five mitochondrial genes in the monocot order Alismatales, all showing marked differences in editing frequencies among taxa. A general tendency to lose edited sites was observed in all taxa, but this tendency was particularly strong in two clades, with most of the edited sites lost in parallel in two different areas of the phylogeny. This pattern is observed in at least four of the five genes analyzed. Except in the groups that show an unusually low editing frequency, the rate of C-to-T changes in edited sites was not significantly higher that in non-edited 3rd codon positions. This may indicate that selection is not actively removing edited sites in nine of the 12 families of the core Alismatales. In all genes but ccmB, a significant correlation was found between frequency of change in edited sites and synonymous substitution rate. In general, taxa with higher substitution rates tend to have fewer edited sites, as indicated by the phylogenetically independent correlation analyses. The elimination of edited sites in groups that lack or have reduced levels of editing could be a result of gene conversion involving a cDNA copy (retroprocessing). If so, this phenomenon could be relatively common in the Alismatales, and may have affected some groups recurrently. Indirect evidence of retroprocessing without a necessary correlation with substitution rate was found mostly in families Alismataceae and Hydrocharitaceae (e.g., groups that suffered a rapid elimination of all their edited sites, without a change in substitution rate).ConclusionsThe effects of substitution rate, selection, and/or gene conversion on the dynamics of edited sites in plant mitochondria remain poorly understood. Although we found an inverse correlation between substitution rate and editing frequency, this correlation is partially obscured by gene retroprocessing in lineages that have lost most of their edited sites. The presence of processed paralogs in plant mitochondria deserves further study, since most evidence of their occurrence is circumstantial.

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Section: Resultsmentioning

confidence: 99%

Are substitution rates and RNA editing correlated?

et al. 2010

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“…RNA editing in plant mitochondria or chloroplasts commonly involves post‐transcriptional substitution of cytidine by uridine (C‐to‐U) or, less commonly, uridine by cytidine (Gray, 1996, 2009; Maier et al. , 1996; Mulligan et al.…”

Section: Rna Editing and The Evolution Of Ppr Genesmentioning

confidence: 99%

The evolution of RNA editing and pentatricopeptide repeat genes

2011

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SummaryThe pentatricopeptide repeat (PPR) is a degenerate 35-amino-acid structural motif identified from analysis of the sequenced genome of the model plant Arabidopsis thaliana. From the wealth of sequence information now available from plant genomes, the PPR protein family is now known to be one of the largest families in angiosperm species, as most genomes encode 400-600 members. As the number of PPR genes is generally only c. 10-20 in other eukaryotic organisms, including green algae, the family has obviously greatly expanded during land plant evolution. This provides a rare opportunity to study selection pressures driving a 50-fold expansion of a single gene family. PPR proteins are sequence-specific RNA-binding proteins involved in many aspects of RNA processing in organelles. In this review, we will summarize our current knowledge about the evolution of PPR genes, and will discuss the relevance of the dramatic expansion in the family to the functional diversification of plant organelles, focusing primarily on RNA editing.

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“…In many cases, editing events cause non-silent mutations and changes in amino acid sequences, generation of initiation or termination codons, and elimination of stop codons. This posttranscriptional modification process creates translatable mature mRNAs that are essential for protein function (Gray, 2009;Maier et al, 1996).…”

Section: Introductionmentioning

confidence: 99%