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Post-transcriptional Regulation in Plant Organelles

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 November 2021) | Viewed by 9059

Special Issue Editor

Graduate School of Informatics, Nagoya University, Nagoya, Japan
Interests: coordinated gene expression between the organelles and nuclear genomes; RNA-binding protein; post-transcriptional regulation in plastids and mitochondria; physcomitrella patens; arabidopsis thaliana; plastid and mitochondrial genomics; RNA editing; RNA splicing; RNA stability; retrograde signaling

Special Issue Information

Dear Colleagues,

Mitochondria and plastids are essential organelles for the survival of the plant cell. They were evolved from the endosymbionts derived from ancestral free-living prokaryotes. During the course of evolution of endosymbiont-host cells, mitochondria and plastids acquired unique own genomes and expression systems distinct from those of their endosymbionts. Most plant organellar genes are often co-transcribed as long polycistronic precursor RNAs, which are then extensively processed into shorter RNA species (via RNA splicing, RNA editing and RNA cleavage, etc.), each of which accumulates at the steady-state RNA levels within the organelles. Post-transcriptional RNA processing represents an important step in the control of plant organellar gene expression and is accomplished mostly by nuclear-encoded proteins. In the last two decades, a plenty of organellar RNA-related proteins were identified as posttranscriptional regulatory factors, and some of their functions were characterized. However, molecular mechanisms underlying the posttranscriptional regulation remain not fully understood. Currently, a wide range of analyses on this topic are in progress.

This Special Issue will bring together updated research articles and reviews on post-transcriptional regulation in intracellular organelles of green algae and plants.

Prof. Dr. Mamoru Sugita
Guest Editor

Manuscript Submission Information

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Keywords

  • Mitochondria and plastids
  • Gene expression and regulation
  • RNA editing
  • RNA splicing
  • RNA cleavage
  • RNA stabilization
  • RNA maturation
  • RNA-binding proteins
  • Small RNA

Published Papers (4 papers)

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Research

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22 pages, 5118 KiB  
Article
MISF2 Encodes an Essential Mitochondrial Splicing Cofactor Required for nad2 mRNA Processing and Embryo Development in Arabidopsis thaliana
by Tan-Trung Nguyen, Corinne Best, Sofia Shevtsov, Michal Zmudjak, Martine Quadrado, Ron Mizrahi, Hagit Zer, Hakim Mireau and Oren Ostersetzer-Biran
Int. J. Mol. Sci. 2022, 23(5), 2670; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23052670 - 28 Feb 2022
Cited by 4 | Viewed by 1890
Abstract
Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous [...] Read more.
Mitochondria play key roles in cellular energy metabolism in eukaryotes. Mitochondria of most organisms contain their own genome and specific transcription and translation machineries. The expression of angiosperm mtDNA involves extensive RNA-processing steps, such as RNA trimming, editing, and the splicing of numerous group II-type introns. Pentatricopeptide repeat (PPR) proteins are key players in plant organelle gene expression and RNA metabolism. In the present analysis, we reveal the function of the MITOCHONDRIAL SPLICING FACTOR 2 gene (MISF2, AT3G22670) and show that it encodes a mitochondria-localized PPR protein that is crucial for early embryo development in Arabidopsis. Molecular characterization of embryo-rescued misf2 plantlets indicates that the splicing of nad2 intron 1, and thus respiratory complex I biogenesis, are strongly compromised. Moreover, the molecular function seems conserved between MISF2 protein in Arabidopsis and its orthologous gene (EMP10) in maize, suggesting that the ancestor of MISF2/EMP10 was recruited to function in nad2 processing before the monocot–dicot divergence ~200 million years ago. These data provide new insights into the function of nuclear-encoded factors in mitochondrial gene expression and respiratory chain biogenesis during plant embryo development. Full article
(This article belongs to the Special Issue Post-transcriptional Regulation in Plant Organelles)
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19 pages, 19685 KiB  
Article
CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts
by Xiuming Li, Wenzhen Luo, Wen Zhou, Xiaopeng Yin, Xuemei Wang, Xiujin Li, Chenchen Jiang, Qingqing Zhang, Xiaojing Kang, Aihong Zhang, Yi Zhang and Congming Lu
Int. J. Mol. Sci. 2021, 22(23), 12639; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222312639 - 23 Nov 2021
Cited by 6 | Viewed by 1515
Abstract
Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its [...] Read more.
Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5′ ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism. Full article
(This article belongs to the Special Issue Post-transcriptional Regulation in Plant Organelles)
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15 pages, 3173 KiB  
Article
Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing
by Marine Guilcher, Arnaud Liehrmann, Chloé Seyman, Thomas Blein, Guillem Rigaill, Benoit Castandet and Etienne Delannoy
Int. J. Mol. Sci. 2021, 22(20), 11297; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222011297 - 19 Oct 2021
Cited by 4 | Viewed by 2746
Abstract
Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, [...] Read more.
Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, however, when it comes to understanding the interplay between the various steps of plastid gene expression. Here, we describe a protocol to study the plastid transcriptome using nanopore sequencing. In the leaf of Arabidopsis thaliana, with about 1.5 million strand-specific reads mapped to the chloroplast genome, we could recapitulate most of the complexity of the plastid transcriptome (polygenic transcripts, multiple isoforms associated with post-transcriptional processing) using virtual Northern blots. Even if the transcripts longer than about 2500 nucleotides were missing, the study of the co-occurrence of editing and splicing events identified 42 pairs of events that were not occurring independently. This study also highlighted a preferential chronology of maturation events with splicing happening after most sites were edited. Full article
(This article belongs to the Special Issue Post-transcriptional Regulation in Plant Organelles)
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Review

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11 pages, 2065 KiB  
Review
PARN-like Proteins Regulate Gene Expression in Land Plant Mitochondria by Modulating mRNA Polyadenylation
by Takashi Hirayama
Int. J. Mol. Sci. 2021, 22(19), 10776; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910776 - 05 Oct 2021
Cited by 3 | Viewed by 2216
Abstract
Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The [...] Read more.
Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The polyadenylation status of mRNA is critical for its stability and translation in mitochondria. In this short review, I focus on recent advances in understanding the mechanisms regulating mRNA polyadenylation in plant mitochondria, including the role of poly(A)-specific ribonuclease-like proteins (PARNs). Accumulating evidence suggests that plant mitochondria have unique regulatory systems for mRNA poly(A) status and that PARNs play pivotal roles in these systems. Full article
(This article belongs to the Special Issue Post-transcriptional Regulation in Plant Organelles)
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