Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures

Jiang, Yan; Fan, Shilong; Song, Min Kyoung; Yu, Jianing; Yu, Shuangxing

doi:10.4238/2012.april.19.4

Cited by 26 publications

(12 citation statements)

References 38 publications

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“…However, although closely related, not every C–T difference between M. polymorpha and P. endiviifolia coding regions reflects an actual editing site because only sites that are important for protein function seem to undergo editing. Editing frequently results in radical amino acid changes, an exchange of amino acids with clearly different physicochemical properties, which could impact protein function (Maier et al 1996; Jiang et al 2012) (fig. 3).…”

Section: Resultsmentioning

confidence: 99%

“…Nevertheless, it is common in land plants where it occurs at frequencies that vary across lineages. Seed plant plastids typically exhibit 26–54 editing sites (Wakasugi et al 1996; Tillich et al 2006; Jiang et al 2012). By contrast, the fern Adiantum capillus-veneris (Wolf et al 2004) and the hornwort Anthoceros formosae (Kugita et al 2003) harbor hundreds of sites that are post-transcriptionally modified by editing.…”

Section: Introductionmentioning

confidence: 99%

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The Chloroplast Genome of Pellia endiviifolia: Gene Content, RNA-Editing Pattern, and the Origin of Chloroplast Editing

Grosche

Funk

Maier

et al. 2012

Genome Biology and Evolution

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RNA editing is a post-transcriptional process that can act upon transcripts from mitochondrial, nuclear, and chloroplast genomes. In chloroplasts, single-nucleotide conversions in mRNAs via RNA editing occur at different frequencies across the plant kingdom. These range from several hundred edited sites in some mosses and ferns to lower frequencies in seed plants and the complete lack of RNA editing in the liverwort Marchantia polymorpha. Here, we report the sequence and edited sites of the chloroplast genome from the liverwort Pellia endiviifolia. The type and frequency of chloroplast RNA editing display a pattern highly similar to that in seed plants. Analyses of the C to U conversions and the genomic context in which the editing sites are embedded provide evidence in favor of the hypothesis that chloroplast RNA editing evolved to compensate mutations in the first land plants.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Chloroplast Genome of Pellia endiviifolia: Gene Content, RNA-Editing Pattern, and the Origin of Chloroplast Editing

Grosche

Funk

Maier

et al. 2012

Genome Biology and Evolution

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“…The ppr98 mutant reduces the RNA editing of the atp9 ‐C92 editing site by 30% (Ichinose et al ., ). In Gossypium hirsutum , chloroplast RNA editing sites were identified and predicted to affect secondary and tertiary protein structures (Jiang et al ., ). Also in cotton, mitochondrial RNA editing events were found to have a close relationship with the restoration of cytoplasmic male sterility (CMS) (Suzuki et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation

Xiao

Líu

et al. 2018

New Phytologist

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RNA editing is a post-transcriptional maturation process affecting organelle transcripts in land plants. However, the molecular functions and physiological roles of RNA editing are still poorly understood. Using high-throughput sequencing, we identified 692 RNA editing sites in the Gossypium hirsutum mitochondrial genome. A total of 422 editing sites were found in the coding regions and all the edits are cytidine (C) to uridine (U) conversions. Comparative analysis showed that two editing sites in Ghatp1, C1292 and C1415, had a prominent difference in editing efficiency between fiber and ovule. Biochemical and genetic analyses revealed that the two vital editing sites were important for the interaction between the α and β subunits of ATP synthase, which resulted in ATP accumulation and promoted cell growth in yeast. Ectopic expression of C1292, C1415, or doubly edited Ghatp1 in Arabidopsis caused a significant increase in the number of trichomes in leaves and root length. Our results indicate that editing at C1292 and C1415 sites in Ghatp1 is crucial for ATP synthase to produce sufficient ATP for cotton fiber cell elongation. This work extends our understanding of RNA editing in atp1 and ATP synthesis, and provides insights into the function of mitochondrial edited Atp1 protein in higher plants.

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“…For example, editing of the second position of the ACG codon at 5’ end of transcripts will create an AUG initiation codon [22,23], and editing of the first position of CAA, CAG and CGA will create stop codons [23]. RE is common in CPs and editing patterns have been studied in crops such as maize [24,25], sugarcane [26], rice [27], pea [28], tomato [26], cotton [29] and black pine [30]. …”

Section: Introductionmentioning

confidence: 99%

Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome

Lin

Kuo

et al. 2015

PLoS ONE

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We performed deep sequencing of the nuclear and organellar genomes of three mungbean genotypes: Vigna radiata ssp. sublobata TC1966, V. radiata var. radiata NM92 and the recombinant inbred line RIL59 derived from a cross between TC1966 and NM92. Moreover, we performed deep sequencing of the RIL59 transcriptome to investigate transcript variability. The mungbean chloroplast genome has a quadripartite structure including a pair of inverted repeats separated by two single copy regions. A total of 213 simple sequence repeats were identified in the chloroplast genomes of NM92 and RIL59; 78 single nucleotide variants and nine indels were discovered in comparing the chloroplast genomes of TC1966 and NM92. Analysis of the mungbean chloroplast transcriptome revealed mRNAs that were affected by transcriptional slippage and RNA editing. Transcriptional slippage frequency was positively correlated with the length of simple sequence repeats of the mungbean chloroplast genome (R2=0.9911). In total, 41 C-to-U editing sites were found in 23 chloroplast genes and in one intergenic spacer. No editing site that swapped U to C was found. A combination of bioinformatics and experimental methods revealed that the plastid-encoded RNA polymerase-transcribed genes psbF and ndhA are affected by transcriptional slippage in mungbean and in main lineages of land plants, including three dicots (Glycine max, Brassica rapa, and Nicotiana tabacum), two monocots (Oryza sativa and Zea mays), two gymnosperms (Pinus taeda and Ginkgo biloba) and one moss (Physcomitrella patens). Transcript analysis of the rps2 gene showed that transcriptional slippage could affect transcripts at single sequence repeat regions with poly-A runs. It showed that transcriptional slippage together with incomplete RNA editing may cause sequence diversity of transcripts in chloroplasts of land plants.

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Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures

Cited by 26 publications

References 38 publications

The Chloroplast Genome of Pellia endiviifolia: Gene Content, RNA-Editing Pattern, and the Origin of Chloroplast Editing

The Chloroplast Genome of Pellia endiviifolia: Gene Content, RNA-Editing Pattern, and the Origin of Chloroplast Editing

Two pivotal RNA editing sites in the mitochondrial atp1mRNA are required for ATP synthase to produce sufficient ATP for cotton fiber cell elongation

Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome

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