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RNA Editing in Plant Genomes: 40th Anniversary
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RNA Editing in Plant Genomes: 40th Anniversary

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 2745

Special Issue Editor

Prof. Dr. Xiaojun Nie

E-Mail Website
Guest Editor
College of Agronomy, Northwest A&F University, Yangling 712100, China
Interests: plant genomics; evolutionary genomics; molecular mechanism underlying abiotic stresses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

RNA editing is a conserved post-transcriptional modification mechanism in which base changes or modifications occur when DNA is transcribed into an RNA molecule. Together with alternative splicing (AS), the RNA editing process provides an indispensable approach for enriching genetic information and diversifying transcriptomes. Since its first identification in the mitochondrial genome of trypanosome in 1986, RNA editing has been widely found in many species, including animals, plants and fungi; it was found that up to 55% of the genetic information in mature mRNA molecules was inconsistent with the initial DNA sequence. In plants, RNA editing is highly prevalent within organelles (mitochondria and chloroplasts) in the form of C–U base transitions (in some plants also U→C), altering the coding sequences of many organellar transcripts; translatable mRNAs can also be produced by creating AUG start sites or eliminating premature stop codons or affect the RNA structure, influence splicing and alter the stability of RNAs, playing a vital role in growth and development, as well as stress adaptation. To celebrate the 40th anniversary of the discovery of RNA editing, the release of a Special Issue, “RNA Editing in Plant Genomes: 40th Anniversary”, is being planned for IJMS, with the aim of including papers concerning novel research data and timely review articles focusing on the study of RNA editing in plant organelles, including, but not limited to, the discovery, functional validation and evolution of RNA editing. We also welcome related study on plant nuclear genomes, as well as novel methods, software and technology papers covering any related topics.

This special issue is upervised by Dr. Xiaojun Nie and assisted by our Topical Advisory Panel Member Dr. Pingchuan Deng (Northwest A&F University).

Dr. Xiaojun Nie
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • RNA editing
  • post-transcription regulation
  • plant organelles
  • chloroplast
  • mitochondria

Published Papers (2 papers)

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16 pages, 8716 KiB  
Article
A Genome-Wide Analysis of the Pentatricopeptide Repeat Protein Gene Family in Two Kiwifruit Species with an Emphasis on the Role of RNA Editing in Pathogen Stress
by Aidi Zhang, Yuhong Xiong, Fang Liu and Xiujun Zhang
Int. J. Mol. Sci. 2023, 24(18), 13700; https://doi.org/10.3390/ijms241813700 - 05 Sep 2023
Cited by 1 | Viewed by 856
Abstract
Kiwifruit is a perennial fruit tree with high nutritional and economic value; however, various pathogen stresses have resulted in reductions in its yield and quality. Pentatricopeptide repeat proteins (PPRs), characterized by tandem repetitions of 35 amino acid motifs, play roles in RNA editing, [...] Read more.
Kiwifruit is a perennial fruit tree with high nutritional and economic value; however, various pathogen stresses have resulted in reductions in its yield and quality. Pentatricopeptide repeat proteins (PPRs), characterized by tandem repetitions of 35 amino acid motifs, play roles in RNA editing, mRNA stability, and splicing. They may also regulate plant development and growth. Nevertheless, the roles of PPRs in plant development and disease resistance remain unclear. In this study, we focused on the roles of PPRs in the fruit development and pathogen stress of kiwifruit and conducted a series of analyses of the PPR gene family in two representative kiwifruit species (Actinidia chinensis (Ach) and Actinidia eriantha (Ace)) with markedly different degrees of disease resistance. A total of 497 and 499 PPRs were identified in Ach and Ace, respectively. All the kiwifruit PPRs could be phylogenetically divided into four subfamilies. There were about 40.68% PPRs predicted to be localized to mitochondria or chloroplasts. A synteny analysis showed that the expansion of the kiwifruit PPRs mainly originated from segmental duplication. Based on RNA-seq data from the fruit over 12 periods of development and maturity, a weighted correlation network analysis suggested that two PPRs, Actinidia20495.t1 and Actinidia15159.t1, may be involved in fruit development and maturation. In addition, we observed different responses with respect to the expression of PPRs and RNA editing between resistant and susceptible kiwifruits following infection with pathogenic bacteria, indicating the regulatory role of PPRs in the stress response via the modulation of RNA editing. The differentially expressed upstream transcription factors of the PPRs were further identified; they may regulate resistance adaption by modulating the expression of the PPRs. Collectively, these results suggest that PPRs play roles in the development and disease resistance of kiwifruit and provide candidate genes for further clarifying the resistance mechanisms in kiwifruits. Full article
(This article belongs to the Special Issue RNA Editing in Plant Genomes: 40th Anniversary)
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17 pages, 6032 KiB  
Article
The ATP Synthase γ Subunit ATPC1 Regulates RNA Editing in Chloroplasts
by Jia Ni, Wenjian Song, Nadia Ahmed Ali, Yayi Zhang, Jiani Xing, Kexing Su, Xingxing Sun and Xiaobo Zhao
Int. J. Mol. Sci. 2023, 24(11), 9203; https://doi.org/10.3390/ijms24119203 - 24 May 2023
Viewed by 1469
Abstract
RNA editing is the process of modifying RNA molecules by inserting, deleting, or substituting nucleotides. In flowering plants, RNA editing occurs predominantly in RNAs encoded by the organellar genomes of mitochondria and chloroplasts, and the main type of editing involves the substitution of [...] Read more.
RNA editing is the process of modifying RNA molecules by inserting, deleting, or substituting nucleotides. In flowering plants, RNA editing occurs predominantly in RNAs encoded by the organellar genomes of mitochondria and chloroplasts, and the main type of editing involves the substitution of cytidine with uridine at specific sites. Abnormal RNA editing in plants can affect gene expression, organelle function, plant growth, and reproduction. In this study, we report that ATPC1, the gamma subunit of ATP synthase in Arabidopsis chloroplasts, has an unexpected role in the regulation of editing at multiple sites of plastid RNAs. The loss of function of ATPC1 severely arrests chloroplast development, causing a pale-green phenotype and early seedling lethality. Disruption of ATPC1 increases the editing of matK-640, rps12-i-58, atpH-3′UTR-13210, and ycf2-as-91535 sites while decreasing the editing of rpl23-89, rpoA-200, rpoC1-488, and ndhD-2 sites. We further show that ATPC1 participates in RNA editing by interacting with known multiple-site chloroplast RNA editing factors, including MORFs, ORRM1, and OZ1. The transcriptome in the atpc1 mutant is profoundly affected, with a pattern of defective expression of chloroplast development-related genes. These results reveal that the ATP synthase γ subunit ATPC1 is involved in multiple-site RNA editing in Arabidopsis chloroplasts. Full article
(This article belongs to the Special Issue RNA Editing in Plant Genomes: 40th Anniversary)
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