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Gene Expression and Modification in Plant Organelles
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Gene Expression and Modification in Plant Organelles

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (1 October 2021) | Viewed by 10530

Special Issue Editor

Prof. Oren Ostersetzer-Biran

E-Mail Website
Guest Editor
The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
Interests: group II introns; splicing; RNA-binding cofactors; OXPHOS; mitogenome expression, mitochondria biogenesis

Special Issue Information

Dear Colleagues,

Mitochondria and chloroplasts serve as principal sites for cellular energy metabolism, and also play key roles in the biosynthesis of numerous essential metabolites for the plant cell. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, plants possess some of the most complex organelle compositions of all known organisms. The organellar genomes in plants are very complex in terms of structure and function. Likewise, the expression of the mitochondrial and plastidial genomes in plants is highly complicated, with much of this control occurring at the post-transcriptional level. RNA-processing events which contribute to organellar expression in plants include trimming, RNA editing and the splicing of introns that disrupt the coding regions of genes required in both organellar translation (i.e., ribosomal or tRNA genes) and proteins required for photosynthetic- or respiratory-mediated functions. These essential RNA-processing steps are mediated by various RNA-binding proteins. Some are related to ancient RNA-binding factors, whereas other are specific to eukaryotes while being prominent to plants. Notably, RNA-processing enzymes comprise a staggering proportion of the plant organelle proteomes. Many appear to be regulated during specific growth and developmental stages, further signifying the importance of the RNA metabolism for organellar biogenesis and plant physiology.

While the complexity of organellar pre-RNA processing has already been documented, the identity of the factors involved in these essential activities and their specific roles in the RNA processing steps they regulate are more obscure.

This Special Issue in Genes (“Gene Expression and Modification in Plant Organelles”) aims to fill the remaining gaps in our understanding of (i) organellar RNA processing, (ii) the molecular functions of nuclear-encoded factors in organellar transcription, RNA metabolism and translation, (iii) how these complex RNA processes are linked to mitochondria or chloroplasts biogenesis and the assembly of respiratory and photosynthetic complexes, and (iv) how these pathways are regulated during plant development and in response to environmental signals. We would greatly appreciate it if you would agree to contribute a research paper, or a comprehensive review (more than 5000 words in the main text), on any aspect related to plant organellar gene expression and modification.

We look forward to your contributions.

Prof. Oren Ostersetzer-Biran
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • Photosynthetic organisms
  • Mitochondria, chloroplasts
  • Gene expression and regulation
  • RNA processing
  • Transcriptomic
  • Epitranscriptomic
  • RNA binding proteins.

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Published Papers (3 papers)

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Research

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17 pages, 2664 KiB  
Article
Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants
by Ting-Ting Zhang, Yang Yang, Xiao-Yu Song, Xin-Yu Gao, Xian-Liang Zhang, Jun-Jie Zhao, Ke-Hai Zhou, Chang-Bao Zhao, Wei Li, Dai-Gang Yang, Xiong-Feng Ma and Zhong-Hu Li
Genes 2021, 12(6), 822; https://doi.org/10.3390/genes12060822 - 27 May 2021
Cited by 8 | Viewed by 2998
Abstract
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as “bridges” in protein synthesis by carrying amino acids. Currently, the [...] Read more.
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as “bridges” in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family. Full article
(This article belongs to the Special Issue Gene Expression and Modification in Plant Organelles)
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Review

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16 pages, 1723 KiB  
Review
Group II Intron-Encoded Proteins (IEPs/Maturases) as Key Regulators of Nad1 Expression and Complex I Biogenesis in Land Plant Mitochondria
by Ron Mizrahi, Sofia Shevtsov-Tal and Oren Ostersetzer-Biran
Genes 2022, 13(7), 1137; https://doi.org/10.3390/genes13071137 - 24 Jun 2022
Cited by 4 | Viewed by 2504
Abstract
Mitochondria are semi-autonomous organelles that produce much of the energy required for cellular metabolism. As descendants of a bacterial symbiont, most mitochondria harbor their own genetic system (mtDNA/mitogenome), with intrinsic machineries for transcription and protein translation. A notable feature of plant mitochondria involves [...] Read more.
Mitochondria are semi-autonomous organelles that produce much of the energy required for cellular metabolism. As descendants of a bacterial symbiont, most mitochondria harbor their own genetic system (mtDNA/mitogenome), with intrinsic machineries for transcription and protein translation. A notable feature of plant mitochondria involves the presence of introns (mostly group II-type) that reside in many organellar genes. The splicing of the mtRNAs relies on the activities of various protein cofactors, which may also link organellar functions with cellular or environmental signals. The splicing of canonical group II introns is aided by an ancient class of RT-like enzymes (IEPs/maturases, MATs) that are encoded by the introns themselves and act specifically on their host introns. The plant organellar introns are degenerated in structure and are generally also missing their cognate intron-encoded proteins. The factors required for plant mtRNA processing are mostly nuclearly-encoded, with the exception of a few degenerated MATs. These are in particular pivotal for the maturation of NADH-dehydrogenase transcripts. In the following review we provide an update on the non-canonical MAT factors in angiosperm mitochondria and summarize the current knowledge of their essential roles in regulating Nad1 expression and complex I (CI) biogenesis during embryogenesis and early plant life. Full article
(This article belongs to the Special Issue Gene Expression and Modification in Plant Organelles)
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22 pages, 1194 KiB  
Review
The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods
by Nikolay Manavski, Alexandre Vicente, Wei Chi and Jörg Meurer
Genes 2021, 12(8), 1121; https://doi.org/10.3390/genes12081121 - 24 Jul 2021
Cited by 8 | Viewed by 4287
Abstract
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, [...] Read more.
Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes. Full article
(This article belongs to the Special Issue Gene Expression and Modification in Plant Organelles)
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