Internal editing of the maize chloroplast ndhA transcript restores codons for conserved amino acids.

Maier, Rainer M.; Hoch, Brigitte; Zeltz, Patric; Kössel, Hans

doi:10.1105/tpc.4.5.609

Cited by 80 publications

(25 citation statements)

References 34 publications

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“…Two years later, the RNA editing of the rpl2 transcript was reported in maize, which produced an initiation codon, ATG, derived from ACG [4]. To date, more than 200 higher plant chloroplast genomes have been sequenced, but editing sites were completely detected only in one moss ( Anthoceros formosae ) [5], one fern ( Adiantum capillus-veneris ) [6], two gymnosperm ( Pinus thunbergii and Cycas taitungensis ) [7, 8], seven eudicots ( Atropa belladonna , Solanum lycopersicum , Phalaenopsis aphrodite , Cucumis sativus , Arabidopsis thaliana, Nicotiana tabacum and Gossypium hirsutum ) [9–15], and four monocotyledons ( Oryza sativa , Saccharum officinarum , Triticum aestivum and Zea mays ) [16–18] . …”

Section: Introductionmentioning

confidence: 99%

Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

Huang

Xiao

et al. 2016

BMC Plant Biol

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BackgroundRNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance.ResultsIn this paper, we investigated 82 protein-coding genes in the chloroplast genome of G. biloba and identified 255 editing sites, which is the highest number of RNA editing events reported in a gymnosperm. All of the editing sites were C-to-U conversions, which mainly occurred in the second codon position, biased towards to the U_A context, and caused an increase in hydrophobic amino acids. RNA editing could change the secondary structures of 82 proteins, and create or eliminate a transmembrane region in five proteins as determined in silico. Finally, the evolutionary tendencies of RNA editing in different gene groups were estimated using the nonsynonymous-synonymous substitution rate selection mode.ConclusionsThe G. biloba chloroplast genome possesses the highest number of RNA editing events reported so far in a seed plant. Most of the RNA editing sites can restore amino acid conservation, increase hydrophobicity, and even influence protein structures. Similar purifying selections constitute the dominant evolutionary force at the editing sites of essential genes, such as the psa, some psb and pet groups, and a positive selection occurred in the editing sites of nonessential genes, such as most ndh and a few psb genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0944-8) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

Huang

Xiao

et al. 2016

BMC Plant Biol

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“…In higher plant chloroplasts, editing proceeds by C-to-U conversions at highly specific sites (Hoch et al, 1991;Kudla et al, 1992;reviewed in Bock, 2000). With very few exceptions (Hirose et al, 1996;Kudla and Bock, 1999), the vast majority of known plastid RNA editing events alter the coding properties of the affected transcripts, usually resulting in the restoration of phylogenetically conserved amino acid residues (Maier et al, 1992a(Maier et al, , 1992b. Transgenic experiments creating plants with a noneditable version of a chloroplast transcript have provided direct evidence for the functional importance of plastid RNA editing (Bock et al, 1994).…”

Section: Intron Splicingmentioning

confidence: 99%

Plastid Transcriptomics and Translatomics of Tomato Fruit Development and Chloroplast-to-Chromoplast Differentiation: Chromoplast Gene Expression Largely Serves the Production of a Single Protein

2008

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Plastid genes are expressed at high levels in photosynthetically active chloroplasts but are generally believed to be drastically downregulated in nongreen plastids. The genome-wide changes in the expression patterns of plastid genes during the development of nongreen plastid types as well as the contributions of transcriptional versus translational regulation are largely unknown. We report here a systematic transcriptomics and translatomics analysis of the tomato (Solanum lycopersicum) plastid genome during fruit development and chloroplast-to-chromoplast conversion. At the level of RNA accumulation, most but not all plastid genes are strongly downregulated in fruits compared with leaves. By contrast, chloroplast-to-chromoplast differentiation during fruit ripening is surprisingly not accompanied by large changes in plastid RNA accumulation. However, most plastid genes are translationally downregulated during chromoplast development. Both transcriptional and translational downregulation are more pronounced for photosynthesis-related genes than for genes involved in gene expression, indicating that some low-level plastid gene expression must be sustained in chromoplasts. High-level expression during chromoplast development identifies accD, the only plastid-encoded gene involved in fatty acid biosynthesis, as the target gene for which gene expression activity in chromoplasts is maintained. In addition, we have determined the developmental patterns of plastid RNA polymerase activities, intron splicing, and RNA editing and report specific developmental changes in the splicing and editing patterns of plastid transcripts.

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“…45,46) In chloroplasts, RNA editing is a widespread processing event that creates start and stop codons and, most frequently, alters coding sequences. [47][48][49][50][51] RNA editing in chloroplasts is mostly a cytosine-to-uracil change at the second nucleotide position of the triplet. 52) In transcripts of the tobacco plastid genome, 0.13% of cytosine is changed to uracil.…”

Section: Rna Editingmentioning

confidence: 99%

Plant Acetyl-CoA Carboxylase: Structure, Biosynthesis, Regulation, and Gene Manipulation for Plant Breeding

Sasaki

Nagano

2004

Bioscience, Biotechnology, and Biochemistry

365

285

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Internal editing of the maize chloroplast ndhA transcript restores codons for conserved amino acids.

Cited by 80 publications

References 34 publications

Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

Plastid Transcriptomics and Translatomics of Tomato Fruit Development and Chloroplast-to-Chromoplast Differentiation: Chromoplast Gene Expression Largely Serves the Production of a Single Protein

Plant Acetyl-CoA Carboxylase: Structure, Biosynthesis, Regulation, and Gene Manipulation for Plant Breeding

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