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

Chu, Duan; Wei, Lai

doi:10.1002/pld3.169

Cited by 37 publications

(25 citation statements)

References 33 publications

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“…Therefore, the altered editing of the rpoB -467 site was not the cause of the phenotype of las1 . The chloroplast and mitochondria RNA editing events may be an indication of evolutionary adaptation (Chu and Wei, 2019 ). The rpl2 , rpoB and atpA gene sequences of the chloroplast genomes of different species were analyzed from the perspective of evolution.…”

Section: Discussionmentioning

confidence: 99%

Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype

Liu

Cao

Huang

et al. 2020

Rice

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Background Chloroplast development is coordinately regulated by plastid- and nuclear-encoding genes. Although many regulators have been reported to be involved in chloroplast development, new factors remain to be identified, given the complexity of this process. Results In this study, we characterized a rice mutant lethal albinic seedling 1 ( las1 )form of a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (OsHMBPP) that was targeted to the chloroplasts. The LAS1 mutation caused the albino lethal phenotype in seedlings. Transmission electron microscopy indicated that las1 were defective in early chloroplast development. LAS1 is preferentially expressed in leaves, implying its role in controlling chloroplast development. The expression levels of many chloroplast-encoded genes were altered significantly in las1 . The expression levels of nuclear-encoded gene involved in Chl biosynthesis were also decreased in las1 . We further investigated plastidic RNA editing in las1 and found that the edit efficiency of four chloroplast genes were markly altered. Compared with WT, las1 exhibited defective in biogenesis of chloroplast ribosomes. Conclusions Our results show that LAS1/OsHMBPP plays an essential role in the early chloroplast development in rice.

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Section: Discussionmentioning

confidence: 99%

Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype

Liu

Cao

Huang

et al. 2020

Rice

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“…It is well established that the nonsynonymous or nonsense mutations are overall deleterious and while the synonymous mutations are regarded as neutral. Usually, the nonsynonymous to synonymous ratios are measurements for the adaptiveness of different sets of nonsynonymous mutations [20,21]. Accordingly, we observed that the fixed to polymorphic ratios of nonsynonymous or nonsense mutations are significantly lower than that of synonymous mutations (Fig.…”

Section: Fixed To Polymorphic Ratios Reveal the Weak Selection On Synmentioning

confidence: 67%

Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations

Chu

Wei

2020

BMC Genomics

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Background: Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate. Intuitively, one may hypothesize that those synonymous mutations which increase the tAI values are favored by natural selection. Results: We use the maize (Zea mays) genome to test our assumption. The first supporting evidence is that the tAIincreasing synonymous mutations have higher fixed-to-polymorphic ratios than the tAI-decreasing ones. Next, the DAF (derived allele frequency) or MAF (minor allele frequency) of the former is significantly higher than the latter. Moreover, similar results are obtained when we investigate CAI (codon adaptation index) instead of tAI. Conclusion:The synonymous mutations in the maize genome are not strictly neutral. The tAI-increasing mutations are positively selected while those tAI-decreasing ones undergo purifying selection. This selection force might be weak but should not be automatically ignored.

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“…Editing at these sites resulted in nonsynonymous amino acid substitutions ( Figure S2A ), which are highly conserved among different species as indicated by the result of multiple alignment ( Figure S2B ). Compared with synonymous editing sites, nonsynonymous editing sites commonly showed higher conservation levels as well as editing levels [ 30 , 38 ], and nonsynonymous sites are more essential and functional, suggesting that detection of novel C-to-U editing sites in this study will provide valuable source for rice biological study.…”

Section: Resultsmentioning

confidence: 99%

Detection and Analysis of C-to-U RNA Editing in Rice Mitochondria-Encoded ORFs

Zheng

Wang

Huang

et al. 2020

Plants

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Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA modification and is almost omnipresent in plant chloroplasts and mitochondria. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alterations needs to be investigated further. Here, by means of Sanger sequencing and publicly available RNA-seq data, we identified a total of 569 C-to-U editing sites in rice mitochondria-encoded open reading frames (ORFs), 85.41% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, based on the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 569 C-to-U RNA editing sites in their biological context. More precise information about C-to-U editing sites in rice mitochondria-encoded ORFs will facilitate our investigation on the function of C-to-U editing events in rice and also provide a valid benchmark from rice for the analysis of mitochondria C-to-U editing in other plant species.

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

Cited by 37 publications

References 33 publications

Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype

Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype

Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations

Detection and Analysis of C-to-U RNA Editing in Rice Mitochondria-Encoded ORFs

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