Rna Metabolism and Transcript Regulation

Zmudjak, Michal; Zer, Hagit

doi:10.1002/9781118906583.ch6

Cited by 11 publications

(54 citation statements)

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“…Higher m 6 A signals in mRNAs versus intron and UTR regions (Figures and S3), may be expected from their expression patterns and RNA metabolism in plants mitochondria (see e.g. Grewe et al , ; Zmudjak and Ostersetzer‐Biran, ). As these analyses were performed with rRNA‐depleted organellar RNAs, any conclusions regarding the presence of m 6 A in rRNAs should be taken with care.…”

Section: Resultsmentioning

confidence: 88%

“…The biogenesis of mitochondria in plants is tightly controlled by nuclear loci that regulate organellar gene expression and metabolic functions (reviewed by for example Zmudjak and Ostersetzer‐Biran, ). We have previously shown that the functions of various maturase‐related factors, including nMAT1 (Nakagawa and Sakurai, ; Keren et al , ), nMAT2 (Keren et al , ; Zmudjak et al , ) and nMAT4 (Cohen et al , ), are required for the maturation of different subsets of mitochondrial pre‐RNAs in Arabidopsis mitochondria.…”

Section: Resultsmentioning

confidence: 99%

“…Co‐IPs, coupled to high‐throughput RNA sequencing methods (Dominissini et al , ) provided comprehensive data into the m 6 A landscapes across the transcriptomes of various organisms, and indicated that m 6 A is the most prevalent modification present in eukaryotic mRNAs (Yue et al , ; Burgess et al , ; Liu and Pan, ; Wang et al , ). Unlike pseudouridylation (Ψ), the most abundant post‐transcriptional modification in RNAs (Ge and Yu, ) are C→U exchanges, which are particularly common in plant organelles (Chateigner‐Boutin and Small, ; Barkan and Small, ; Colas des Francs‐Small and Small, ; Hammani and Giege, ; Shikanai, ; Ichinose and Sugita, ; Schallenberg‐Rüdinger and Knoop, ; Zmudjak and Ostersetzer‐Biran, ). m 6 A is not expected to rewire the genetic code for translation (Dai et al , ).…”

Section: Discussionmentioning

confidence: 99%

“…These stages involve both anterograde (nucleus to organelles) and retrograde (organelles to nucleus) signalling cascades (Woodson and Chory, ), but the identity of the messenger molecules involved in these pathways is more elusive. The expression of the mtDNA in plants is complex, particularly at the post‐transcriptional level (reviewed by for example Hammani and Giege, and Zmudjak and Ostersetzer‐Biran, ). While in Animalia, the mtDNAs are symmetrically transcribed in opposite directions, yielding two large polycistronic RNAs, the mitochondrial genes in plants are arranged in many transcription units that undergo extensive processing steps.…”

Section: Introductionmentioning

confidence: 99%

“…splicing) and the conversion of numerous cytidines (C) to uridines (U) by deamination (i.e. mainly C → U RNA editing) (reviewed by Liere et al , ; Small, ; Hammani and Giege, ; Binder et al , ; Gualberto and Newton, ; Zmudjak and Ostersetzer‐Biran, ). These processing steps are required to allow mtRNAs to carry out their functions in protein synthesis, but may also serve as key control points in gene expression, i.e.…”

Section: Introductionmentioning

confidence: 99%

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Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

et al. 2019

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Summary Mitochondria serve as major sites of ATP production and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e. mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the post‐transcriptional level. Following transcription, the polycistronic pre‐RNAs undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6‐methylation of adenosine ribonucleotides (m6A‐RNA) in plant mitochondria. m6A is a prevalent modification in nuclear‐encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6A mediates structural switches that affect RNA stability and/or activity. Using m6A‐pulldown/RNA‐seq (m6A‐RIP‐seq) assays of Arabidopsis and cauliflower mitochondria, we provide information on the m6A‐RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non‐coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6A modifications, N6‐methylation of adenosine residues with mRNAs seem preferably positioned near start codons and may modulate their translatability.

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Section: Resultsmentioning

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

et al. 2019

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MSP1encodes an essential RNA-binding PPR factor required fornad1maturation and complex I biogenesis inArabidopsismitochondria

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Mizrahi

Edris

et al. 2022

Preprint

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Mitochondria are semi-autonomous organelles that serve as hubs for aerobic energy metabolism. The biogenesis of the respiratory (OXPHOS) system relies on nuclear-encoded factors, which regulate the transcription, processing and translation of mitochondrial (mt)RNAs. These include proteins of primordial origin, as well as eukaryotic-type RNA-binding families recruited from the host genomes to function in mitogenome expression. Pentatricopeptide repeat (PPR) proteins constitute a major gene-family in angiosperms that is pivotal in many aspects of mtRNA metabolism, such as editing, splicing or stability. Here, we report the analysis ofMITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1(MSP1, At4g20090), a canonical mitochondria-localized PPR protein that is necessary for mitochondrial biogenesis and embryo-development. Functional complementation confirmed that the phenotypes result from a disruption of theMSP1gene. As a loss-of-function allele ofArabidopsis MSP1leads to seed abortion, we employed an embryo-rescue method for the molecular characterization ofmsp1mutants. Our data show that msp1 embryo-development fails to proceed beyond the heart-torpedo transition stage as a consequence of a severenad1pre-RNA processing-defect, resulting in the loss of respiratory complex I (CI) activity. The maturation of nad1 involves the processing of three RNA-fragments,nad1.1,nad1.2andnad1.3. Based on detailed analyses of the mtRNA profiles in wild-type andmsp1plants, we concluded that through its association with a specific site innad1.1, MSP1 facilitates the generation of its 3'-terminus and stabilizes it - a prerequisite fornad1exons a-b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory machinery during early-plant development.

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The DEAD‐box RNA helicase ZmRH48 is required for the splicing of multiple mitochondrial introns, mitochondrial complex biosynthesis, and seed development in maize

Yang,

Ding,

Liu

et al. 2023

JIPB

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RNA helicases participate in nearly all aspects of RNA metabolism by rearranging RNAs or RNA–protein complexes in an ATP‐dependent manner. Due to the large RNA helicase families in plants, the precise roles of many RNA helicases in plant physiology and development remain to be clarified. Here, we show that mutations in maize (Zea mays) DEAD‐box RNA Helicase 48 (ZmRH48) impair the splicing of mitochondrial introns, mitochondrial complex biosynthesis, and seed development. Loss of ZmRH48 function severely arrested embryogenesis and endosperm development, leading to defective kernel formation. ZmRH48 is targeted to mitochondria, where its deficiency dramatically reduced the splicing efficiency of five cis‐introns (nad5 intron 1; nad7 introns 1, 2, and 3; and ccmFc intron 1) and one trans‐intron (nad2 intron 2), leading to lower levels of mitochondrial complexes I and III. ZmRH48 interacts with two unique PPR proteins, PPR‐SMR1 and SPR2, which are required for the splicing of over half of all mitochondrial introns. PPR‐SMR1 interacts with SPR2, and both proteins interact with P‐type PPR proteins and Zm‐mCSF1 to facilitate intron splicing. These results suggest that ZmRH48 is likely a component of a splicing complex and is critical for mitochondrial complex biosynthesis and seed development.This article is protected by copyright. All rights reserved.

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Rna Metabolism and Transcript Regulation

Cited by 11 publications

References 268 publications

Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

MSP1encodes an essential RNA-binding PPR factor required fornad1maturation and complex I biogenesis inArabidopsismitochondria

The DEAD‐box RNA helicase ZmRH48 is required for the splicing of multiple mitochondrial introns, mitochondrial complex biosynthesis, and seed development in maize

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Rna Metabolism and Transcript Regulation

Cited by 11 publications

References 268 publications

Topologies of N6‐adenosine methylation (m6A) in land plant mitochondria and their putative effects on organellar gene expression

Topologies of N6‐adenosine methylation (m6A) in land plant mitochondria and their putative effects on organellar gene expression

MSP1encodes an essential RNA-binding PPR factor required fornad1maturation and complex I biogenesis inArabidopsismitochondria

The DEAD‐box RNA helicase ZmRH48 is required for the splicing of multiple mitochondrial introns, mitochondrial complex biosynthesis, and seed development in maize

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Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression

Topologies of N⁶‐adenosine methylation (m⁶A) in land plant mitochondria and their putative effects on organellar gene expression