Divergence of RNA editing among Arabidopsis species

Kawabe, Akira; Furihata, Hazuka Y.; Tsujino, Yudai; Kawanabe, Takahiro; Fujii, Sota; Yoshida, Takanori

doi:10.1016/j.plantsci.2018.12.009

Cited by 11 publications

(10 citation statements)

References 60 publications

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“…Although other study also discovered that the loss of editing events in kin species might be due to the changed editing factor (Kawabe et al, 2019), the C-to-T DNA switch found by Edera et al caught our interest. If the advantage of RNA editing is increasing the protein diversity, then the C-to-T-mutated DNA would actually abolish this diversity.…”

Section: Discussionmentioning

confidence: 83%

“…However, their multiple angiosperm study revealed another interesting trend that highly edited cytidines were likely to be replaced with thymidines during genome evolution. Although other study also discovered that the loss of editing events in kin species might be due to the changed editing factor (Kawabe et al, ), the C‐to‐T DNA switch found by Edera et al caught our interest. If the advantage of RNA editing is increasing the protein diversity, then the C‐to‐T‐mutated DNA would actually abolish this diversity.…”

Section: Discussionmentioning

confidence: 89%

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The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

Chu

Wei

2019

Plant Direct

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C‐to‐U RNA editing is the conversion from cytidine to uridine at RNA level. In plants, the genes undergo C‐to‐U RNA modification are mainly chloroplast and mitochondrial genes. Case studies have identified the roles of C‐to‐U editing in various biological processes, but the functional consequence of the majority of C‐to‐U editing events is still undiscovered. We retrieved the deep sequenced transcriptome data in roots and shoots of Arabidopsis thaliana and profiled their C‐to‐U RNA editomes and gene expression patterns. We investigated the editing level and conservation pattern of these C‐to‐U editing sites. The levels of nonsynonymous C‐to‐U editing events are higher than levels of synonymous events. The fraction of nonsynonymous editing sites is higher than neutral expectation. Highly edited cytidines are more conserved at DNA level, and the gene expression levels are correlated with C‐to‐U editing levels. Our results demonstrate that the global C‐to‐U editome is shaped by natural selection and that many nonsynonymous C‐to‐U editing events are adaptive. The editing mechanism might be positively selected and maintained and could have profound effects on the modified RNAs.

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Section: Discussionmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 89%

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

Chu

Wei

2019

Plant Direct

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“…Mutants defective in RNA editing show loss of function of the target gene products. These mutations are sometimes linked to severe phenotypic disorders [16,35,36]. MORF9 is a pivotal factor of the labile plastid RNA editosome complex and participates in a wide range of editing events at multiple sites of plant plastid RNAs.…”

Section: Discussionmentioning

confidence: 99%

MORF9 Functions in Plastid RNA Editing with Tissue Specificity

Tian

Zhang

et al. 2019

IJMS

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RNA editing in plant mitochondria and plastids converts specific nucleotides from cytidine (C) to uridine (U). These editing events differ among plant species and are relevant to developmental stages or are impacted by environmental conditions. Proteins of the MORF family are essential components of plant editosomes. One of the members, MORF9, is considered the core protein of the editing complex and is involved in the editing of most sites in chloroplasts. In this study, the phenotypes of a T-DNA insertion line with loss of MORF9 and of the genetic complementation line of Arabidopsis were analyzed, and the editing efficiencies of plastid RNAs in roots, rosette leaves, and flowers from the morf9 mutant and the wild-type (WT) control were compared by bulk-cDNA sequencing. The results showed that most of the known MORF9-associated plastid RNA editing events in rosette leaves and flowers were similarly reduced by morf9 mutation, with the exception that the editing rate of the sites ndhB-872 and psbF-65 declined in the leaves and that of ndhB-586 decreased only in the flowers. In the roots, however, the loss of MORF9 had a much lower effect on overall plastid RNA editing, with nine sites showing no significant editing efficiency change, including accD-794, ndhD-383, psbZ-50, ndhF-290, ndhD-878, matK-706, clpP1-559, rpoA-200, and ndhD-674, which were reduced in the other tissues. Furthermore, we found that during plant aging, MORF9 mRNA level, but not the protein level, was downregulated in senescent leaves. On the basis of these observations, we suggest that MORF9-mediated RNA editing is tissue-dependent and the resultant organelle proteomes are pertinent to the specific tissue functions.

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“…It is possible that this exchange does not have noticeable impact on the protein function. The variation in RNA editing among Arabidopsis species, affecting functionally less important sites, was recently described [40], but the position 50 of psbZ was uniformly edited in the Arabidopsis species according to this study. As the position 50 of psbZ is completely edited in the model plant A. thaliana, the identification of nuclear factors responsible for the psbZ editing will be possible, which may help to clarify the function of this editing event.…”

Section: Rna Editing In Plastid Transcriptomes Of S Vulgarismentioning

confidence: 53%

Variation in plastid genomes and transcriptomes in the gynodioecious species Silene vulgaris

Krüger

Abeyawardana

Juříček

et al. 2019

Preprint

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Background Gynodioecious species exist in two genders – male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about gender-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious species Silene vulgaris with known CMS candidate genes. Results We generated complete plastid genome sequences from five haplotypes S. vulgaris including the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences of S. vulgaris. Whereas lowland S. vulgaris haplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram. S. vulgaris belongs among Silene species with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in the ndhF gene, which may reflect the adaptation of S. vulgaris to high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two genders. We identified 51 unique C to U editing sites in the plastid genomes of S. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in the psbZ gene was edited only in one of two plastid genomes under study. Conclusions We revealed no significant differences between the genders in plastid transcriptomes of two haplotypes of S. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds of S. vulgaris, although both genders may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of two S. vulgaris haplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes in S. vulgaris.

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Divergence of RNA editing among Arabidopsis species

Cited by 11 publications

References 60 publications

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

MORF9 Functions in Plastid RNA Editing with Tissue Specificity

Variation in plastid genomes and transcriptomes in the gynodioecious species Silene vulgaris

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