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Structural and functional properties of plant mitochondrial F-ATP synthase. Mitochondrion 2020; 53:178-193. [DOI: 10.1016/j.mito.2020.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
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Koike T, Kato S, Shimamoto Y, Kitamura K, Kawano S, Ueda K, Mikami T. Mitochondrial DNA Variation Follows a Geographic Pattern in Japanese Beech Species. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1998.tb00682.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Matsunaga M, Nagano H, Mikami T, Kubo T. Large 3' UTR of sugar beet rps3 is truncated in cytoplasmic male-sterile mitochondria. PLANT CELL REPORTS 2011; 30:231-238. [PMID: 20711727 DOI: 10.1007/s00299-010-0912-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 07/13/2010] [Accepted: 08/05/2010] [Indexed: 05/29/2023]
Abstract
Genomic alteration near or within mitochondrial gene is often associated with cytoplasmic male sterility (CMS). Its influence on the expression of the mitochondrial gene was proposed as one of the possible causes of CMS. In sugar beet mitochondrial rps3, whose downstream 1,056-bp region contains Norf246, an apparently non-functional open reading frame (ORF), was deleted in CMS mitochondria. In our previous study, normal rps3 (3.8 kb), CMS rps3 (2.7 kb), and Norf246 (3.8 and 0.9 kb) were shown to be transcribed. The present study was conducted to determine whether the deletion affected gene expression. Reverse transcription (RT)-PCR analysis revealed the co-transcription of rps3 and Norf246. By circularized RNA (CR) RT-PCR analysis, the 5' and 3' termini of the 3.8- and the 0.9-kb transcripts were determined. The results suggested that the 3.8-kb transcripts were the rps3 mRNA bearing ~464-base 5' untranslated region (UTR) and ~1,508-base 3' UTR, whereas no functional ORF was observed in the 0.9-kb transcripts. CR-RT-PCR revealed that the 3' UTR of the 2.7-kb transcripts was reduced to ~460 bases. However, no difference in the accumulation of RPS3 polypeptide and RNA editing was detected by protein gel blot analysis and cDNA sequencing. Although the deleted region encoded the truncated-atp9 that was edited, no influence on the pattern and frequency of RNA editing of genuine atp9 was evident. The results eliminated rps3 as a candidate for the CMS gene, making preSatp6, a unique ORF fused with CMS atp6, the sole CMS-associated region in sugar beet.
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Affiliation(s)
- Muneyuki Matsunaga
- Laboratory of Genetic Engineering, Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo 060-8589, Japan
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Mower JP, Palmer JD. Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genomics 2006; 276:285-93. [PMID: 16862402 DOI: 10.1007/s00438-006-0139-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 05/23/2006] [Indexed: 11/27/2022]
Abstract
RNA editing is a process that modifies the information in transcripts of almost all angiosperm mitochondrial protein-coding genes. In order to determine the frequency and distribution of mitochondrial RNA editing in Beta vulgaris, cDNAs were sequenced and compared to the published genome sequence. 357 C to U conversions were identified across the 31 known protein genes and pseudogenes in Beta, the fewest so far for a plant mitochondrial genome. Editing patterns in the putative gene orf518 indicate that it is most likely a functional ccmC homolog, indicating that patterns of editing can be a useful determinant of gene functionality. orf518 also contains a triplicated repeat region whose members are nearly identical yet differentially edited, most likely due to differences in the sequence context of the editing sites. In addition, we show that partial editing in Beta is common at silent editing sites but rare at nonsilent editing sites, extending previous observations to a complete plant mitochondrial genome. Finally, the degree of partial editing observed for certain genes was dependent on the choice of primers used, demonstrating that care must be taken when designing primers for use in editing studies.
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Affiliation(s)
- Jeffrey P Mower
- Department of Biology, Indiana University, Bloomington, IN 47405, USA. [corrected]
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Satoh M, Kubo T, Nishizawa S, Estiati A, Itchoda N, Mikami T. The cytoplasmic male-sterile type and normal type mitochondrial genomes of sugar beet share the same complement of genes of known function but differ in the content of expressed ORFs. Mol Genet Genomics 2004; 272:247-56. [PMID: 15340837 DOI: 10.1007/s00438-004-1058-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Accepted: 08/13/2004] [Indexed: 10/26/2022]
Abstract
The complete nucleotide sequence (501,020 bp) of the mitochondrial genome from cytoplasmic male-sterile (CMS) sugar beet was determined. This enabled us to compare the sequence with that previously published for the mitochondrial genome of normal, male-fertile sugar beet. The comparison revealed that the two genomes have the same complement of genes of known function. The rRNA and tRNA genes encoded in the CMS mitochondrial genome share 100% sequence identity with their respective counterparts in the normal genome. We found a total of 24 single nucleotide substitutions in 11 protein genes encoded by the CMS mitochondrial genome. However, none of these seems to be responsible for male sterility. In addition, several other ORFs were found to be actively transcribed in sugar beet mitochondria. Among these, Norf246 was observed to be present in the normal mitochondrial genome but absent from the CMS genome. However, it seems unlikely that the loss of Norf246 is causally related to the expression of CMS, because previous studies on mitochondrial translation products failed to detect the product of this ORF. Conversely, the CMS genome contains four transcribed ORFs (Satp6presequence, Scox2-2 , Sorf324 and Sorf119) which are missing from the normal genome. These ORFs, which are potential candidates for CMS genes, were shown to be generated by mitochondrial genome rearrangements.
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Affiliation(s)
- M Satoh
- Laboratory of Genetic Engineering, Graduate School of Agriculture, Hokkaido University, N-9 W-9, 060-8589 Kita-ku, Sapporo, Japan
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Kato S, Yamaguchi H, Shimamoto Y, Mikami T. The chloroplast genomes of azuki bean and its close relatives: a deletion mutation found in weed azuki bean. Hereditas 2000; 132:43-8. [PMID: 10857258 DOI: 10.1111/j.1601-5223.2000.00043.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A physical map of the azuki bean (Vigna angularis cv. Erimo-shozu) chloroplast DNA (cpDNA) was constructed by localising the cleavage sites of PstI, SalI, SmaI, SacI, KpnI, PvuII and XhoI. The resulting map is more similar to the cpDNA-maps of two Vigna species (mung bean, V. radiata, and V. nakashimae) than to common bean (Phaseolus vulgaris) cpDNA map. Azuki bean was originally classified in the genus Phaseolus, and the inclusion of this taxon in the genus Vigna is a recent taxonomic decision. Our result is thus in favour of the taxonomic placement of azuki bean in the same genus as V. nakashimae and mung bean. We also found that a weed-form accession of azuki bean has a 96-bp deletion relative to the cultivar Erimo-shozu. The 96-bp deletion is located between the trnS-UGA and psbC genes in the large single-copy region of the chloroplast genome. This deletion is flanked by imperfect 9-bp direct repeats, suggesting that the deletion was a result of intra-molecular recombination mediated by these direct repeats.
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Affiliation(s)
- S Kato
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Senda M, Onodera Y, Mikami T. Cytoplasmic diversity in leaf beet cultivars as revealed by mitochondrial DNA analysis. Hereditas 1998; 128:127-32. [PMID: 9652232 DOI: 10.1111/j.1601-5223.1998.00127.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mitochondrial (mt) DNA restriction fragment length polymorphisms are convenient markers for identifying cytoplasmic variation among plant cultivars. In an attempt to detect new cytoplasmic genotypes useful for sugarbeet breeding, we have compared the hybridization patterns of mtDNA from three groups of cultivated beets, viz. leaf beet, garden beet, and fodder beet. Utilized as probes were the two sugarbeet mtDNA clones that were capable of distinguishing normal fertile and different sources of male-sterile cytoplasms from one another. The analysis allowed the identification of four chondriome types among 14 leaf beet cultivars examined. Two out of the four chondriome types were found to be different from the previously described fertile or male-sterile chondriome type. Our results thus indicate that leaf beet cultivars and landraces make up the primary cytoplasmic gene pool of the sugarbeet.
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Affiliation(s)
- M Senda
- Gene Research Center, Hirosaki University, Japan
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Ran Z, Michaelis G. Mapping of a chloroplast RFLP marker associated with the CMS cytoplasm of sugar beet (Beta vulgaris). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:836-840. [PMID: 24169966 DOI: 10.1007/bf00223889] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/1995] [Accepted: 03/31/1995] [Indexed: 06/02/2023]
Abstract
The Owen cytoplasm of male-sterile sugar beet is associated with several alterations of mitochondrial DNA and one additional HindIII site of chloroplast DNA. The region of this HindIII site has been cloned and sequenced. The site maps in a small reading frame (orf32) close to the ycf7 (orf31) gene in the petG-psbE region of chloroplast DNA. Possible functional implications of the results are discussed. The chloroplast RFLP marker described could be useful for studies on chloroplast-mitochondrial interactions, CMS of sugar beet, and the origin of the Owen cytoplasm.
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Affiliation(s)
- Z Ran
- Botanisches Institut der Universität Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
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Kubo T, Satoh Y, Muro T, Kinoshita T, Mikami T. Physical and gene organization of mitochondrial DNA from the fertile cytoplasm of sugarbeet (Beta vulgaris L.). Curr Genet 1995; 28:235-41. [PMID: 8529269 DOI: 10.1007/bf00309782] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have constructed a complete physical map of the mitochondrial genome from the male-fertile cytoplasm of sugarbeet. The entire sequence complexity can be represented on a single circular master chromosome of 358 kb. This master chromosome contains three copies of one recombinationally active repeat sequence, with two copies in direct orientation and the other in inverted orientation. The positions of the rRNA genes and of 23 polypeptide genes, determined by filter hybridization, are scattered throughout the genome, with triplicate rrn26 genes located partially or entirely within the recombination-repeat elements. Three ribosomal-protein genes (rps1A, rps14 and rps19) were found to be absent from sugarbeet mtDNA. Our results also reveal that at least six regions homologous with cDNA are dispersed in the mitochondrial genome.
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Affiliation(s)
- T Kubo
- Laboratory of Genetic Engineering, Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Senda M, Onodera Y, Kinoshita T, Mikami T. Mitochondrial gene variation and phylogenetic relationships in the genus Beta. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:914-919. [PMID: 24173044 DOI: 10.1007/bf00222903] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/1994] [Accepted: 11/22/1994] [Indexed: 06/02/2023]
Abstract
Restriction fragment length polymorphisms (RFLPs) for three mitochondrial genes, coxI, coxII and atpA, were used to determine mitochondrial (mt) DNA diversity in 21 accessions of the genus Beta representing wild and cultivated species. On the basis of distribution of the RFLP patterns these Beta genotypes were assigned into six distinct chondriome groups. A high degree of heterogeneity was found to exist between the mitochondrial genomes of the sugarbeet cultivar and the wild species of Procumbentes section. The polymorphic fragments from wild Beta species were cloned and subjected to fine mapping. We found that most of the RFLPs are due to sequence rearrangements rather than point mutations. Our data also suggest that the close linkage between coxII and coxI is taxonomically localized to an evolutionary lineage that led to Vulgares and Corollinae species but not to Procumbentes species. This linkage is most likely to have arisen via the mutation(s) that inserted the DNA segment containing coxI downstream of coxII in the common ancestor of Vulgares and Corollinae species. The results are discussed with regard to the taxonomic and phylogenetic relationships of the Beta species.
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Affiliation(s)
- M Senda
- Plant Breeding Institute, Faculty of Agriculture, Hokkaido University, 060, Sapporo, Japan
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Xue Y, Collin S, Davies DR, Thomas CM. Differential screening of mitochondrial cDNA libraries from male-fertile and cytoplasmic male-sterile sugar-beet reveals genome rearrangements at atp6 and atpA loci. PLANT MOLECULAR BIOLOGY 1994; 25:91-103. [PMID: 8003700 DOI: 10.1007/bf00024201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
As part of a strategy to define differences in genome organization and expression between cytoplasmic male-sterile (CMS) and male-fertile (MF) sugar-beet mitochondria, cDNA libraries from both mitochondrial genotypes were constructed. Preliminary screening with ribosomal RNA gene probes identified candidate cDNA clones corresponding to structural genes. In addition, reciprocal hybridization experiments were performed using labelled first-strand cDNA to identify uniquely transcribed sequences. One cDNA clone (pYC700) is unique to CMS mitochondria and is located upstream of the F0F1-ATPase subunit 6 gene (atp6). Another cDNA clone (pYC130), when used as a probe in northern hybridization analysis, revealed novel transcript profiles in CMS sugar-beet mitochondria. Sequence analysis of this cDNA showed strong homology with the F0F1-ATPase subunit alpha (atpA) coding sequences from several higher plants. The atp6 and atpA loci from each genotype were cloned and the genomic organization, DNA sequence and transcription of each locus was studied. Differences in the transcript profiles of each gene are a consequence of genomic rearrangements 5' to the coding sequence.
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Affiliation(s)
- Y Xue
- AFRC Institute of Plant Science Research, John Innes Research Centre, Norwich, UK
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Sane AP, Nath P, Sane PV. Mitochondrial ATP synthase genes may be implicated in cytoplasmic male sterility inSorghum bicolor. J Biosci 1994. [DOI: 10.1007/bf02703467] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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