The unique topologies ofN⁶-Adenosine methylation (m⁶A) in land-plant mitochondria and their putative effects on organellar gene-expression

Abstract

Mitochondria are the main source of ATP production and also contribute to many other processes central to cellular function. Mitochondrial activities have been linked with growth, differentiation and aging. As relicts of bacterial endosymbionts, these organelles contain their own genetic system (i.e., mitogenome or mtDNA). The expression of the mtDNA in plants is complex, particularly at the posttranscriptional level. Following transcription, the polycistronic pre-RNAs in plant mitochondria are processed into individual RNAs, which then undergo extensive modifications, as trimming, splicing and C→U editing, before being translated by organellar ribosomes. Our study focuses on N 6 -methylation of Adenosine ribonucleotides (m 6 A-RNA) in plant mitochondria. m 6 A is the most common modification in eukaryotic mRNAs. The biological significance of this highly dynamic modification is under investigation, but it's widely accepted that m 6 A mediates structural switches that affect RNA stability and activity. By performing m 6 A-pulldown/RNA-seq (m 6 A-RIP-seq) analyses of Arabidopsis and cauliflower mitochondrial transcripts (mtRNAs), we provide with detail information on the m 6 A landscapes in angiosperms mitochondria. The results indicate that m 6 A targets different types of mtRNAs, including coding sequences, UTRs, introns and non-coding RNA species. While introns and noncoding-RNAs undergo multiple m 6 A modifications along the transcript, in mRNAs m 6 A-modifications are preferably positioned near start-codons, and may modulate the translatability of the m 6 A-modified transcripts. The products of the mitochondrial orf25 and orfB genes are FO components in the plant F1FO ATP synthase. FEBS Lett, 540, 201-205. . (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. A. and Erlacher, M.D. (2016) Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code. Nucleic Acids Res, 44, 852-862.

So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes

“…This finding is consistent with other experiments demonstrating the additive negative effect of multiple m 6 A residues on translation (Slobodin et al, 2017) and the depletion of m 6 A from efficiently expressed yeast and mammalian housekeeping genes (Schwartz et al, 2014). The negative correlation between methylated ORF and translation was observed in Xenopus embryos (Qi et al, 2016), maize (Luo et al, 2020), and in vitro tested plant mitochondrial transcripts (Murik et al, 2020), indicating an evolutionarily conserved effect. Indeed, the negative global relationship between the translation efficiency and m 6 A is apparent only when the latter is located within ORFs (Mao et al, 2019).…”

N6‐Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis

“…Accumulating evidence has indicated that dysregulation of m 6 A RNA methylation influences development in yeast (Yadav and Rajasekharan, 2017), meiosis in mice (Bushkin et al , 2019), fertility in Drosophila (Kan et al , 2017) and carcinogenesis in human cells (Dai et al , 2018; Pan et al , 2018). Recently, it has also been established that m 6 A methylation plays vital roles during the different stages of plant development, including embryo development (Bodi et al , 2012; Zhong et al , 2008), leaf morphogenesis (Arribas‐Hernández et al , 2018; Arribas‐Hernández et al , 2020; Růžička et al , 2017; Shen et al , 2016), trichome branching (Arribas‐Hernández et al , 2018; Bodi et al , 2012; Vespa et al , 2004; Wei et al , 2018), floral transition (Duan et al , 2017; Song et al , 2021), root growth (Chen et al , 2018; Růžička et al , 2017), the early degeneration of microspores in Oryza sativa (rice) (Zhang et al , 2019), fruit ripening in Solanum lycopersicum (tomato) (Zhou et al , 2019) and organellar gene expression (Murik et al , 2020). These findings clearly indicate that m 6 A RNA methylation plays crucial roles in the development of plants and animals.…”

Insights into the mitochondrial transcriptome landscapes of two Brassicales plant species,Arabidopsis thaliana(var. Col-0) andBrassica oleracea(var. botrytis)

“…While Arabidopsis serves as a prime model system for plant molecular genetics, cauliflower is employed for biochemical analysis of plant mitochondrial RNA metabolism (Grewe, et al 2014, Neuwirt, et al 2005, Sultan, et al 2016a. To generate the transcriptome maps of Arabidopsis and cauliflower mitochondria, we used total mtRNA extracted from highly enriched mitochondria preparations obtained from Arabidopsis seedlings and cauliflower inflorescence (Murik et al 2019). The mtRNA from each plant species was subjected to Illumina sequencing (see Materials and Methods), which resulted in approximately 6.2 million mapped reads for At-mtRNA (SRA no.…”

“…Mapping the Arabidopsis mtRNA-seq reads (SRA no. SRX4110179) (Murik, et al 2019) to mitochondrial genomic annotation and RT-qPCR data ( Figs. 1 and 2) demonstrated differential expression of the 21 mitochondria-encoded genes required for OXPHOS, as well as various ribosomal subunits (Fig 1c-e).…”