A mitochondrial gene involved in cytochrome c maturation (ccmC) is expressed as a precursor with a long NH2-terminal extension in sugar beet

Kitazaki, Kazuyoshi; Y, Nomoto; Aoshima, Akihiro; Mikami, Tetsuo; Kubo, Tomohiko

doi:10.1016/j.jplph.2008.09.002

Cited by 7 publications

(4 citation statements)

References 19 publications

(21 reference statements)

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“…Although Beta vulgaris ccmC is widely reported to be a pseudogene, it is transcribed, edited, and translated (Mower and Palmer 2006; Kitazaki et al 2009) and is scored as functionally present here. Arabidopsis ccmFn is split into two genes, but the two halves are counted as a single gene here.…”

Section: Resultsmentioning

confidence: 99%

Evidence against Equimolarity of Large Repeat Arrangements and a Predominant Master Circle Structure of the Mitochondrial Genome from a Monkeyflower (Mimulus guttatus) Lineage with Cryptic CMS

Mower

Case

Floro

et al. 2012

Genome Biology and Evolution

113

125

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Despite intense investigation for over 25 years, the in vivo structure of plant mitochondrial genomes remains uncertain. Mapping studies and genome sequencing generally produce large circular chromosomes, whereas electrophoretic and microscopic studies typically reveal linear and multibranched molecules. To more fully assess the structure of plant mitochondrial genomes, the complete sequence of the monkeyflower (Mimulus guttatus DC. line IM62) mitochondrial DNA was constructed from a large (35 kb) paired-end shotgun sequencing library to a high depth of coverage (∼30×). The complete genome maps as a 525,671 bp circular molecule and exhibits a fairly conventional set of features including 62 genes (encoding 35 proteins, 24 transfer RNAs, and 3 ribosomal RNAs), 22 introns, 3 large repeats (2.7, 9.6, and 29 kb), and 96 small repeats (40–293 bp). Most paired-end reads (71%) mapped to the consensus sequence at the expected distance and orientation across the entire genome, validating the accuracy of assembly. Another 10% of reads provided clear evidence of alternative genomic conformations due to apparent rearrangements across large repeats. Quantitative assessment of these repeat-spanning read pairs revealed that all large repeat arrangements are present at appreciable frequencies in vivo, although not always in equimolar amounts. The observed stoichiometric differences for some arrangements are inconsistent with a predominant master circular structure for the mitochondrial genome of M. guttatus IM62. Finally, because IM62 contains a cryptic cytoplasmic male sterility (CMS) system, an in silico search for potential CMS genes was undertaken. The three chimeric open reading frames (ORFs) identified in this study, in addition to the previously identified ORFs upstream of the nad6 gene, are the most likely CMS candidate genes in this line.

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Section: Resultsmentioning

confidence: 99%

Evidence against Equimolarity of Large Repeat Arrangements and a Predominant Master Circle Structure of the Mitochondrial Genome from a Monkeyflower (Mimulus guttatus) Lineage with Cryptic CMS

Mower

Case

Floro

et al. 2012

Genome Biology and Evolution

113

125

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“…The fused rps2 of maize is translated, then the C-terminal extension is cleaved off, but it can be detected as a solitary polypeptide [86]. Sugar beet has a unique ccmC gene in which the conserved translational initiation codon is lost, but instead, the chimeric N-terminal extension consists of a duplicated segment of atp9 and a sequence of unknown origin [90] (Figure 2(b)). The mature CCMC polypeptide is yielded from the fused polypeptide by cleavage of the N-terminal extension [90].…”

Section: Why Do Most Of the Unique Orfs Not Matter In Angiosperm Mitomentioning

confidence: 99%

“…Sugar beet has a unique ccmC gene in which the conserved translational initiation codon is lost, but instead, the chimeric N-terminal extension consists of a duplicated segment of atp9 and a sequence of unknown origin [90] (Figure 2(b)). The mature CCMC polypeptide is yielded from the fused polypeptide by cleavage of the N-terminal extension [90]. It has been suggested that the putative cleavage site may precede SerPro-Leu, by analogy with atp6.…”

Section: Why Do Most Of the Unique Orfs Not Matter In Angiosperm Mitomentioning

confidence: 99%

Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome

Kitazaki

Kubo

2010

Journal of Botany

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The angiosperm mitochondrial genome is the largest and least gene-dense among the eukaryotes, because its intergenic regions are expanded. There seems to be no functional constraint on the size of the intergenic regions; angiosperms maintain the large mitochondrial genome size by a currently unknown mechanism. After a brief description of the angiosperm mitochondrial genome, this review focuses on our current knowledge of the mechanisms that control the maintenance and alteration of the genome. In both processes, the control of homologous recombination is crucial in terms of site and frequency. The copy numbers of various types of mitochondrial DNA molecules may also be controlled, especially during transmission of the mitochondrial genome from one generation to the next. An important characteristic of angiosperm mitochondria is that they contain polypeptides that are translated from open reading frames created as byproducts of genome alteration and that are generally nonfunctional. Such polypeptides have potential to evolve into functional ones responsible for mitochondrially encoded traits such as cytoplasmic male sterility or may be remnants of the former functional polypeptides.

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“…CcmC plays a pivotal role in the maturation of cytochrome c and is translated as a long precursor with an N-extension. Our analysis identified 31 C-to-U RNA editing events in N-extension and cmC-homologous region (ccmC-core region), which contribute to the conservation of amino acid sequence ( Kitazaki et al, 2009 ). RNA editing serves as a crucial post-transcriptional modification mechanism which greatly influence the expression and function of mitochondrial gene.…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements

Xie,

Liu,

Guo

et al. 2024

Front. Genet.

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Mitochondria are semi-autonomous organelles in eukaryotic cells with their own genome. Plant mitogenomes differ from animal mitogenomes in size, structure, and repetitive DNA sequences. Despite larger sizes, plant mitogenomes do not have significantly more genes. They exhibit diverse structures due to variations in size, repetitive DNA, recombination frequencies, low gene densities, and reduced nucleotide substitution rates. In this study, we analyzed the mitochondrial genome of Stemona sessilifolia using Nanopore and Illumina sequencing. De-novo assembly and annotation were conducted using Unicycler, Geseq, tRNAscan-SE and BLASTN, followed by codon usage, repeat sequence, RNA-editing, synteny, and phylogenetic analyses. S. sessilifolia’s mitogenome consisted of one linear contig and six circular contigs totaling 724,751 bp. It had 39 protein-coding genes, 27 tRNA genes, and 3 rRNA genes. Transfer of chloroplast sequences accounted for 13.14% of the mitogenome. Various analyses provided insights into genetic characteristics, evolutionary dynamics, and phylogenetic placement. Further investigations can explore transferred genes’ functions and RNA-editing’s role in mitochondrial gene expression in S. sessilifolia.

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A mitochondrial gene involved in cytochrome c maturation (ccmC) is expressed as a precursor with a long NH2-terminal extension in sugar beet

Cited by 7 publications

References 19 publications

Evidence against Equimolarity of Large Repeat Arrangements and a Predominant Master Circle Structure of the Mitochondrial Genome from a Monkeyflower (Mimulus guttatus) Lineage with Cryptic CMS

Evidence against Equimolarity of Large Repeat Arrangements and a Predominant Master Circle Structure of the Mitochondrial Genome from a Monkeyflower (Mimulus guttatus) Lineage with Cryptic CMS

Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome

Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements

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