Plant organellar RNA editing: what 30 years of research has revealed

The Plant Journal, Journal Year: 2019, Volume and Issue: 101(5), P. 1040 - 1056

Published: Oct. 20, 2019

The central dogma in biology defines the flow of genetic information from DNA to RNA protein. Accordingly, molecules generally accurately follow sequences genes which they are transcribed. This rule is transgressed by editing, creates products that differ their templates. Analyses landscapes terrestrial plants have indicated editing (in form C-U base transitions) highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and some also U→C) alter coding many organellar transcripts can produce translatable mRNAs creating AUG start sites or eliminating premature stop codons, affect structure, influence splicing stability RNAs. RNA-binding proteins at heart post-transcriptional expression. C-to-U process plant involves numerous nuclear-encoded factors, been identified as pentatricopeptide repeat (PPR) target a sequence-specific manner. In this review we report on major discoveries organelles, since it was first documented 30 years ago.

Language: Английский

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Variation in protein gene and intron content among land plant mitogenomes

Mitochondrion, Journal Year: 2020, Volume and Issue: 53, P. 203 - 213

Published: June 12, 2020

Language: Английский

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RNA Editing and Its Roles in Plant Organelles

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: Sept. 29, 2021

RNA editing, a vital supplement to the central dogma, yields genetic information on products that are different from their DNA templates. The conversion of C-to-U in mitochondria and plastids is main kind editing plants. Various factors have been demonstrated be involved editing. In this minireview, we summarized mechanisms plant organelles. Recently, rapid development deep sequencing has revealed many events organelles, further reviewed these identified through data. Numerous studies shown plays essential roles diverse processes, such as biogenesis chloroplasts mitochondria, seed development, stress hormone responses. Finally, discussed functions

Language: Английский

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Advancing organelle genome transformation and editing for crop improvement

Plant Communications, Journal Year: 2021, Volume and Issue: 2(2), P. 100141 - 100141

Published: Jan. 10, 2021

Plant cells contain three organelles that harbor DNA: the nucleus, plastids, and mitochondria. Plastid transformation has emerged as an attractive platform for generation of transgenic plants, also referred to transplastomic plants. genomes have been genetically engineered improve crop yield, nutritional quality, resistance abiotic biotic stresses, well recombinant protein production. Despite many promising proof-of-concept applications, plants not commercialized date. Sequence-specific nuclease technologies are widely used precisely modify nuclear genomes, but these tools applied edit organelle because efficient homologous recombination system in plastids facilitates plastid genome editing. Unlike transformation, successful genetic higher plant mitochondrial was tested several research group, However, stepwise progress made modifying genes their transcripts, thus enabling study functions. Here, we provide overview advances editing improvement, discuss bottlenecks future development technologies.

Language: Английский

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Chloroplast gene expression: Recent advances and perspectives

Plant Communications, Journal Year: 2023, Volume and Issue: 4(5), P. 100611 - 100611

Published: May 4, 2023

Chloroplasts evolved from an ancient cyanobacterial endosymbiont more than 1.5 billion years ago. During subsequent coevolution with the nuclear genome, chloroplast genome has remained independent, albeit strongly reduced, its own transcriptional machinery and distinct features, such as chloroplast-specific innovations to gene expression complicated post-transcriptional processing. Light activates of genes via mechanisms that optimize photosynthesis, minimize photodamage, prioritize energy investments. Over past few years, studies have moved stage describing phases explore underlying mechanisms. In this review, we focus on recent advances emerging principles govern in land plants. We discuss PPR protein engineering biotechnological impacts RNA research, new techniques for elucidating molecular expression, some important aspects improving crop yield stress tolerance. also remaining biological mechanistic questions be answered future.

Language: Английский

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C-to-U and U-to-C: RNA editing in plant organelles and beyond

Journal of Experimental Botany, Journal Year: 2022, Volume and Issue: 74(7), P. 2273 - 2294

Published: Dec. 17, 2022

The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous 'errors' that are corrected at level RNA transcript copies. genes encoded endosymbiotic would not function properly if their transcripts were altered by site-specific cytidine-to-uridine (C-to-U) exchanges additional reverse U-to-C hornworts, lycophytes, ferns. These peculiar processes editing, re-establishing genetic information could alternatively be present organelle genome level, has spurred much research over >30 years. Lately new studies have revealed interesting insights, notably on biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U vice versa. Here, I will summarize prominent findings lately contributed our better understanding these phenomena introducing an added layer processing cells. Some this recent progress is based successful functional expression editing factors bacteria mammalian approaches recapitulated natural horizontal gene transfer through which some protist lineages seem acquired adapted them functionally own purposes.

Language: Английский

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Characterisation of the complete mitochondrial genome of Taraxacum mongolicum revealed five repeat-mediated recombinations

Plant Cell Reports, Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 12, 2023

Language: Английский

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The complete mitochondrial genome of Amorphophallus albus and development of molecular markers for five Amorphophallus species based on mitochondrial DNA

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: June 21, 2023

Amorphophallus albus is an herbaceous, cormous, perennial plant used as a food source and traditional medicine in Asia.In this study, we assembled annotated the complete mitochondrial genome (mitogenome) of A. albus. Then analyzed repeated elements plastid sequences (MTPTs), predicted RNA editing sites protein-coding genes (PCGs). Lastly, inferred phylogenetic relationships other angiosperms based on PCGs, designed two molecular markers DNA.The mitogenome consists 19 circular chromosomes. And total length 537,044 bp, with longest chromosome measuring 56,458 bp shortest 12,040 bp. We identified 36 (PCGs), 21 tRNA genes, 3 rRNA mitogenome. Additionally, DNAs (MTPTs) 20 MTPTs between organelle genomes, combined 22,421 accounting for 12.76% plastome. Besides, 676 C to U high confidence using Deepred-mt. Furthermore, extensive genomic rearrangement was observed related mitogenomes. conducted analyses PCGs determine evolutionary angiosperms. Finally, developed validated markers, Ai156 Ai976, intron regions (nad2i156 nad4i976) respectively. The discrimination success rate 100 % validation experiments five widely grown konjac species. Our results reveal multi-chromosome albus, will facilitate identification genus.

Language: Английский

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Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts

Nucleus, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 29, 2024

Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome a flexible manner. It has been challenging task to identify beneficial sites from sea of total events. The functional Ser>Gly auto-recoding site insect Adar gene uneditable Ser codons ancestral nodes, indicating selective advantage having an editable status. Here, we extended this case study more metazoan species, also looked for all Drosophila recoding events with potential synonymous codons. Interestingly, D. melanogaster, abundant nonsynonymous is enriched that have counterparts, but suggests orthologous other species are not necessarily edited. use versus codon smart way infer editing, priority might be given these studies due feasibility construct allele. Our proposes idea narrow down candidates sites. Meanwhile, stress matched transcriptomes needed verify conservation during evolution.

Language: Английский

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Comparative genomics and phylogenetic analysis of mitochondrial genomes of Neocinnamomum

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: March 6, 2025

Neocinnamomum plants are considered a promising feedstock for biodiesel in China, due to the richness long-chain fatty acids (LCFAs) found their seeds. However, mitochondrial genome (mitogenome) of this genus has not yet been systematically described, and exploration species relationships within using mitogenome sequences is also an uncharted territory. This hindered our understanding diversity evolutionary Neocinnamomum. In study, total 24 individuals representing seven distinct taxa from were subjected Illumina sequencing, N. delavayi was sequenced Oxford Nanopore sequencing technology. We successfully assembled delavayi, which 778,066 bp size exhibits single circular structure. The analysis identified 659 dispersed repeats, 211 simple sequence repeats (SSRs), 30 tandem mitogenome. Additionally, 37 homologous fragments, totaling 9929 bp, between plastid (plastome). codons 41 protein-coding genes (PCGs) had preference ending A/T, codon usage bias majority these influenced by natural selection pressures. Comparative genomic revealed low collinearity significant gene rearrangements species. Phylogenetic resulted classification into six clades, contradicting previous findings based on complete plastomes nuclear ribosomal cistron (nrDNA). PCGs individuals, 86 mutation events identified, included three indels 83 SNPs. Notably, ccmC underwent positive pairwise comparisons pairs. Furthermore, 748 RNA editing sites predicted study enriches knowledge mitogenomes family Lauraceae, provides valuable data foundation evolution research, genetic resource conservation, molecular breeding

Language: Английский

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