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Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression in Plants
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Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression in Plants

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 (30 January 2024) | Viewed by 6287

Special Issue Editors

Prof. Dr. Víctor Quesada

E-Mail Website
Guest Editor
Instituto de Bioingeniería, Universidad Miguel Hernandez de Elche, 3202 Elche, Spain
Interests: genetics; plant development; abiotic stress; arabidopsis; chloroplast biogenesis; mTERF; organelle gene expression
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Pedro Robles

E-Mail Website
Guest Editor
Instituto de Bioingeniería, Universidad Miguel Hernandez de Elche, 3202 Elche, Spain
Interests: plant genetics; leaf and fruit development; Arabidopsis; organelles and development, mTERF, chlororibosome; organelles stress sensors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genetic material of mitochondria and chloroplasts is the result of an intense process of genomic erosion undergone by the genomes of the endosymbionts from which these organelles originate. The relatively few genes now remaining in the organelles code for proteins involved in organellar gene expression (OGE), photosynthesis or energy production. Despite the small gene complement of chloroplasts and mitochondria, OGE is a complex process, particularly evident in plastids since they have retained a prokaryotic gene-expression apparatus combined with eukaryotic innovations. The regulation of OGE is crucial to chloroplasts and mitochondria biogenesis and, hence, to plant development, growth and to allow plants to adjust to physiological demands and environmental cues. Multiple levels of OGE regulation have been described in recent years encompassing different molecular mechanisms of control acting on RNA transcription, splicing, editing, trimming, translation or through post-translational modifications. Despite this, the molecular mechanisms governing OGE are far from being fully understood.

This Special Issue aims to summarize the state-of-the-art knowledge on the transcriptional and post-transcriptional regulation of gene expression in plant organelles, from RNA transcription to post-translational control mechanisms. We encourage the publication of both original research articles and review papers, not only from a purely molecular point of view, but also from a genetics and mutational perspective.

Prof. Dr. Víctor Quesada
Prof. Dr. Pedro Robles
Guest Editors

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

  • chloroplasts and mitochondria
  • organelle nucleoids
  • transcriptional regulation in plant organelles
  • post-transcriptional regulation in plant organelles
  • translational and post-translational control in plant organelles
  • RNA binding proteins
  • RNA metabolism in plant organelles

Published Papers (4 papers)

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Research

15 pages, 3043 KiB  
Article
YUCCA2 (YUC2)-Mediated 3-Indoleacetic Acid (IAA) Biosynthesis Regulates Chloroplast RNA Editing by Relieving the Auxin Response Factor 1 (ARF1)-Dependent Inhibition of Editing Factors in Arabidopsis thaliana
by Zi-Ang Li, Yi Li, Dan Liu, David P. Molloy, Zhou-Fei Luo, Hai-Ou Li, Jing Zhao, Jing Zhou, Yi Su, Ruo-Zhong Wang, Chao Huang and Lang-Tao Xiao
Int. J. Mol. Sci. 2023, 24(23), 16988; https://doi.org/10.3390/ijms242316988 - 30 Nov 2023
Viewed by 1084
Abstract
Although recent research progress on the abundant C-to-U RNA editing events in plant chloroplasts and mitochondria has uncovered many recognition factors and their molecular mechanisms, the intrinsic regulation of RNA editing within plants remains largely unknown. This study aimed to establish a regulatory [...] Read more.
Although recent research progress on the abundant C-to-U RNA editing events in plant chloroplasts and mitochondria has uncovered many recognition factors and their molecular mechanisms, the intrinsic regulation of RNA editing within plants remains largely unknown. This study aimed to establish a regulatory relationship in Arabidopsis between the plant hormone auxin and chloroplast RNA editing. We first analyzed auxin response elements (AuxREs) present within promoters of chloroplast editing factors reported to date. We found that each has more than one AuxRE, suggesting a potential regulatory role of auxin in their expression. Further investigation unveiled that the depletion of auxin synthesis gene YUC2 reduces the expression of several editing factors. However, in yuc2 mutants, only the expression of CRR4, DYW1, ISE2, and ECD1 editing factors and the editing efficiency of their corresponding editing sites, ndhD-2 and rps14-149, were simultaneously suppressed. In addition, exogenous IAA and the overexpression of YUC2 enhanced the expression of these editing factors and the editing efficiency at the ndhD-2 and rps14-149 sites. These results suggested a direct effect of auxin upon the editing of the ndhD-2 and rps14-149 sites through the modulation of the expression of the editing factors. We further demonstrated that ARF1, a downstream transcription factor in the auxin-signaling pathway, could directly bind to and inactivate the promoters of CRR4, DYW1, and ISE2 in a dual-luciferase reporter system, thereby inhibiting their expression. Moreover, the overexpression of ARF1 in Arabidopsis significantly reduced the expression of the three editing factors and the editing efficiency at the ndhD-2 and rps14-149 sites. These data suggest that YUC2-mediated auxin biosynthesis governs the RNA-editing process through the ARF1-dependent signal transduction pathway. Full article
(This article belongs to the Special Issue Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression in Plants)
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13 pages, 4859 KiB  
Article
Alteration of Mitochondrial Transcript Expression in Arabidopsis thaliana Using a Custom-Made Library of Pentatricopeptide Repeat Proteins
by Lilian Vincis Pereira Sanglard, Ian D. Small and Catherine Colas des Francs-Small
Int. J. Mol. Sci. 2023, 24(17), 13233; https://doi.org/10.3390/ijms241713233 - 26 Aug 2023
Viewed by 806
Abstract
Pentatricopeptide repeat (PPR) proteins are considered a potential tool for manipulating organelle gene expression in plants because they can recognise a wide range of different RNA sequences, and the molecular basis for this sequence recognition is partially known and understood. A library of [...] Read more.
Pentatricopeptide repeat (PPR) proteins are considered a potential tool for manipulating organelle gene expression in plants because they can recognise a wide range of different RNA sequences, and the molecular basis for this sequence recognition is partially known and understood. A library of redesigned PPR proteins related to restorer-of-fertility proteins was created and transformed into plants in order to target mitochondrial transcripts. Ninety different variants tested in vivo showed a wide range of phenotypes. One of these lines, which displayed slow growth and downward curled leaves, showed a clear reduction in complex V. The phenotype was due to a specific cleavage of atp1 transcripts induced by a modified PPR protein from the library, validating the use of this library as a source of mitochondrial ‘mutants’. This study is a step towards developing specific RNA targeting tools using PPR proteins that can be aimed at desired targets. Full article
(This article belongs to the Special Issue Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression in Plants)
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19 pages, 5782 KiB  
Article
Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species
by Hongyu Cai, Yachao Ren, Juan Du, Lingyun Liu, Lianxiang Long and Minsheng Yang
Int. J. Mol. Sci. 2023, 24(16), 12954; https://doi.org/10.3390/ijms241612954 - 19 Aug 2023
Viewed by 1060
Abstract
In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were [...] Read more.
In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were typical circular genomes 156,860–157,025 bp in length, with 37.58–37.6% GC content. Repeat analysis showed that the Deutzia species had 41–45 scattered repeats and 199–201 simple sequence repeats. Comparative genomic and pi analyses indicated that the genomes are conservative and that the gene structures are stable. According to the phylogenetic tree, Deutzia species appear to be closely related to Kirengeshoma palmata and Philadelphus. By combining chloroplast genomic and transcriptomic analyses, 29–31 RNA editing events and 163–194 orthologous genes were identified. The ndh, rpo, rps, and atp genes had the most editing sites, and all RNA editing events were of the C-to-U type. Most of the orthologous genes were annotated to the chloroplast, mitochondria, and nucleus, with functions including energy production and conversion, translation, and protein transport. Genes related to the biosynthesis of monoterpenoids and flavonoids were also identified from the transcriptome of Deutzia spp. Our results will contribute to further studies of the genomic information and potential uses of the Deutzia spp. Full article
(This article belongs to the Special Issue Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression in Plants)
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15 pages, 4298 KiB  
Article
DEK48 Is Required for RNA Editing at Multiple Mitochondrial Sites and Seed Development in Maize
by Dalin Yang, Shi-Kai Cao, Huanhuan Yang, Rui Liu, Feng Sun, Le Wang, Miaodi Wang and Bao-Cai Tan
Int. J. Mol. Sci. 2022, 23(6), 3064; https://doi.org/10.3390/ijms23063064 - 12 Mar 2022
Cited by 6 | Viewed by 2133
Abstract
In flowering plants, C-to-U RNA editing can be critical to normal functions of mitochondrion-encoded proteins. Mitochondrial C-to-U RNA editing is facilitated by many factors from diverse protein families, of which the pentatricopeptide repeat (PPR) proteins play an important role. Owing to their large [...] Read more.
In flowering plants, C-to-U RNA editing can be critical to normal functions of mitochondrion-encoded proteins. Mitochondrial C-to-U RNA editing is facilitated by many factors from diverse protein families, of which the pentatricopeptide repeat (PPR) proteins play an important role. Owing to their large number and frequent embryo lethality in mutants, functions of many PPRs remain unknown. In this study, we characterized a mitochondrion-localized DYW-type PPR protein, DEK48, functioning in the C-to-U RNA editing at multiple mitochondrial transcripts in maize. Null mutation of Dek48 severely arrests embryo and endosperm development, causing a defective kernel (dek) phenotype, named dek48. DEK48 loss of function abolishes the C-to-U editing at nad3-185, -215, and nad4-376, -977 sites and decreases the editing at 11 other sites, resulting in the alteration of the corresponding amino acids. Consequently, the absence of editing caused reduced assembly and activity of complex I in dek48. Interestingly, we identified a point mutation in dek48-3 causing a deletion of the Tryptophan (W) residue in the DYW motif that abolishes the editing function. In sum, this study reveals the function of DEK48 in the C-to-U editing in mitochondrial transcripts and seed development in maize, and it demonstrates a critical role of the W residue in the DYW triplet motif of DEK48 for the C-to-U editing function in vivo. Full article
(This article belongs to the Special Issue Transcriptional and Post-transcriptional Regulation of Organellar Gene Expression in Plants)
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