An Unusual Mitochondrial atp9-rpl16 Cotranscript Found in the Maternal Distorted Leaf Mutant of Arabidopsis thaliana: Implication of GUG as an Initiation Codon in Plant Mitochondria

Sakamoto, Wataru; Tan, Siang Hee; Murata, Minoru; Motoyoshi, Fusao

doi:10.1093/oxfordjournals.pcp.a029261

Cited by 15 publications

(8 citation statements)

References 16 publications

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“…RNA editing resulted in generation of new start or stop codons has been reported in both humans and plants [27,28] (also see reviews in [6,29]). In this study, a systemic search was performed to identify novel start or stop codons generated by RNA editing in nuclear CDSs.…”

Section: Resultsmentioning

confidence: 99%

RNA editing of nuclear transcripts in Arabidopsis thaliana

et al. 2010

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BackgroundRNA editing is a transcript-based layer of gene regulation. To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear transcripts of Arabidopsis (Arabidopsis thaliana) was performed.ResultsMPSS (massively parallel signature sequencing) and PARE (parallel analysis of RNA ends) data retrieved from public databases were utilized, focusing on one-base-conversion editing. Besides cytidine (C)-to-uridine (U) editing in mitochondrial transcripts, many nuclear transcripts were found to be diversely edited. Interestingly, a sizable portion of these nuclear genes are involved in chloroplast- or mitochondrion-related functions, and many editing events are tissue-specific. Some editing sites, such as adenosine (A)-to-U editing loci, were found to be surrounded by peculiar elements. The editing events of some nuclear transcripts are highly enriched surrounding the borders between coding sequences (CDSs) and 3′ untranslated regions (UTRs), suggesting site-specific editing. Furthermore, RNA editing is potentially implicated in new start or stop codon generation, and may affect alternative splicing of certain protein-coding transcripts. RNA editing in the precursor microRNAs (pre-miRNAs) of ath-miR854 family, resulting in secondary structure transformation, implies its potential role in microRNA (miRNA) maturation.ConclusionsTo our knowledge, the results provide the first global view of RNA editing in plant nuclear transcripts.

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Section: Resultsmentioning

confidence: 99%

RNA editing of nuclear transcripts in Arabidopsis thaliana

et al. 2010

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“…Finally, the present study shows that CMS-specific alterations occur in the region upstream of the atp9 gene in CMS 'Tournefortii-Stiewe'. Rearrangements in the atp9 region are not only involved in male sterility but may also induce other phenotypic aberrations, as reported for the distorted leaf mutant of A. thaliana (Sakamoto et al 1997).…”

Section: Discussionmentioning

confidence: 65%

Alloplasmic male sterility in Brassica napus (CMS 'Tournefortii-Stiewe') is associated with a special gene arrangement around a novel atp9 gene

2003

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To identify regions of the mitochondrial genome potentially involved in the expression of alloplasmic 'Tournefortii-Stiewe' cytoplasmic male sterility (CMS) in Brassica napus, transcripts of 25 mitochondrial genes were analysed in fertile and near isogenic male-sterile plants (BC(8) generation). Differences were detected in the transcription of genes for subunit 9 of ATP synthase (atp9), cytochrome b (cob) and subunit 2 of NADH dehydrogenase (nad2). Structural analysis of these gene regions revealed differences in genome organisation around atp9 between male-sterile and fertile plants. Three atp9 genes, two of which were hitherto unknown, are present in the mitochondria of CMS plants, and rearrangements upstream of one of these genes have generated a chimeric 193-codon ORF, designated orf193. This region is transcribed as a CMS specific bi-cistronic mRNA of 1.58 kb comprising orf193 and atp9. The level of the aberrant 1.58-kb transcript is reduced in plants restored to fertility by as yet uncharacterized nuclear genes. orf193 encodes a polypeptide of 22.7 kDa which exhibits partial sequence identity to the subunit 6 of the ATP synthase complex. However, as it forms an uninterrupted ORF with one of the newly discovered atp9 genes it may also be translated as a chimeric 30.2-kDa protein. It is likely that either or both gene products interfere with the function or assembly of the mitochondrial F(0)F(1)-ATP synthase, thus impairing the highly ATP-dependent process of pollen development. The novel molecular features of alloplasmic 'Tournefortii-Stiewe' CMS are discussed with respect to the other known mechanisms of CMS in B. napus.

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“…We manually corrected the annotation of genes to address start codons created by RNA editing of ACG to the start codon AUG, and editing of GCG to the alternative start codon GUG (see results for details). Three genes display atypical start codons: rpl16 uses a GUG start codon (Sakamoto et al 1997); rps19 uses a GUG start codon created by RNA editing GCG, seen also in Pinus strobus AJP33554.1; matR appears to use an unusual GGG start codon, seen also in Cycas taitungensis YP_001661429.1 (Chaw et al 2008) and Pinus strobus AJP33535.1. The gene sdh4 was missed by automatic annotation, as its coding sequence was found to overlap with cox3 by 73 bp on the same strand.…”

Section: Annotationmentioning

confidence: 99%

“…Annotating plant mitochondrial genomes is also challenging, due to numerous features of plant mitochondria that are not typical of most organisms. For one, RNA editing of C-to-U is pervasive, and this process creates AUG start codons by editing ACG to AUG (Hiesel et al 1989) or by editing GCG to GUG, an alternative start codon used by some plant mitochondrial genes (Sakamoto et al 1997). RNA editing can also create stop codons in a similar fashion.…”

Section: Introductionmentioning

confidence: 99%

Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

Jackman¹,

Coombe²,

Warren³

et al. 2019

Preprint

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Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), the largest complete mitochondrial genome of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

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An Unusual Mitochondrial atp9-rpl16 Cotranscript Found in the Maternal Distorted Leaf Mutant of Arabidopsis thaliana: Implication of GUG as an Initiation Codon in Plant Mitochondria

Cited by 15 publications

References 16 publications

RNA editing of nuclear transcripts in Arabidopsis thaliana

RNA editing of nuclear transcripts in Arabidopsis thaliana

Alloplasmic male sterility in Brassica napus (CMS 'Tournefortii-Stiewe') is associated with a special gene arrangement around a novel atp9 gene

Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

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