RNA editing machinery in plant organelles

Yan, Junjie; Zhang, Qunxia; Yin, Ping

doi:10.1007/s11427-017-9170-3

Cited by 82 publications

(83 citation statements)

References 56 publications

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“…RNA analyses have shown that RNA editing (mainly in the form of C-to-U base conversions) is highly widespread within the chloroplasts of land plants. During this process, numerous C-to-U conversions alter the coding sequences of chloroplast mRNAs, regulate RNA secondary structures that influences the splicing and/or stability of RNAs, or generate translational start sites (AUG) [ 47 , 48 ]. All of these RNA metabolic events depend on many nucleus-encoded proteins, most of which likely arose during coevolution between the host and endosymbiont.…”

Section: The Characteristics Of Chloroplast Gene Expressionmentioning

confidence: 99%

The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

Zhang

et al. 2020

IJMS

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Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes and gene-expression machinery. Most genes from the prokaryotic ancestors of chloroplasts were transferred into the nucleus over the course of evolution. However, the importance of chloroplast gene expression in environmental stress responses have recently become more apparent. Here, we discuss the emerging roles of the distinct chloroplast gene expression processes in plant responses to environmental stresses. For example, the transcription and translation of psbA play an important role in high-light stress responses. A better understanding of the connection between chloroplast gene expression and environmental stress responses is crucial for breeding stress-tolerant crops better able to cope with the rapidly changing environment.

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Section: The Characteristics Of Chloroplast Gene Expressionmentioning

confidence: 99%

The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

Zhang

et al. 2020

IJMS

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“…In higher plants, RNA editing usually occurs in plastids and mitochondria and plays important roles in organelle biogenesis, environmental adaptation and development. Yan et al discuss the divergent roles of the plant RNA editing factors such as pentatricopeptide repeat (PPR) proteins, multiple organelle RNA editing factors (MORF, also known as RIP), organelle RNA recognition motif (ORRM) containing proteins, protoporphyrinogen IX oxidase 1 (PPO1) and organelle zinc finger 1 (OZ1) (Yan et al, 2018).…”

Section: Non-coding Rnas: the Long And The Short Of Themmentioning

confidence: 99%

Plant non-coding RNAs and epigenetics

Wang

2018

Sci. China Life Sci.

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“…Numerous studies have demonstrated that RNA editing plays an important role in various plant fundamental processes, such as organelle biogenesis, adaptation to environmental changes, and signal transduction [8][9][10]. A number of factors are involved in plant RNA editing, and considered to interact with one another to form a large protein complex, termed as editsome, PLS subfamily members of pentatrico peptide repeat (PPR) proteins function in site recognition of the target C, multiple organelle RNA editing factors (MORF) family members are components of the RNA editosome and also required for RNA editing at multiple editing sites in plants [11,12]. Almost all the PPR proteins are localized in either chloroplasts or mitochondria where those proteins participate in different facets of RNA metabolism such as RNA splicing, RNA stability, and translational initiation [13].…”

Section: Introductionmentioning

confidence: 99%

A comprehensive study on chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis

zhang

Fang

Jiang

et al. 2020

Preprint

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Abstract Background RNA editing is a post-transcriptional modification that complement variation at the DNA level. Until now, different RNA editing systems were found in the major eukaryotic lineages. However, the evolution trajectory in plant chloroplast remains unclear. To gain a better understanding of RNA editing in plant chloroplast, in this study, based on publicly available RNA-seq data across three clades (fern, gymnosperm, and angiosperm), we provided a detailed analysis of RNA editing events in plant chloroplasts and discussed the evolution of RNA editing in land plants. Results There were a total of 5,389 editing sites located in leaf chloroplast identified across 21 plants after rigorous screening. We found that the cluster of RNA editing sites across 21 plants complied with the phylogenetic tree based on linked protein sequences approximately, there is a common phenomenon that more editing sites occurred in ancient plants for all the three clades. Statistics results revealed that majority (~ 95%) of the editing events resulted in non-synonymous codon changes, RNA editing occurred in second codon position was mainly the largest, and RNA editing caused an overall increase in hydrophobicity of the resulting proteins. The analyses also revealed that there was an uneven distribution of editing sites among species, genes, and codon positions, the average RNA editing extent varied among different plants as well as genes, a lowest RNA editing extent (0.43) was detected in Selaginella moellendorffii. Finally, we found that the loss of editing sites along angiosperm evolution is mainly occurring by reduce of cytosines content, where fern plants has the highest cytosine content. Conclusions Many of the RNA sites identified in our study have not been previously reported and provide a valuable data set for future research community. Our findings also provide valuable information for evolution of RNA editing in plants.

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RNA editing machinery in plant organelles

Cited by 82 publications

References 56 publications

The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress

Plant non-coding RNAs and epigenetics

A comprehensive study on chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis

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