Transfer RNA genes in the mitochondrial genome from a liverwort,<i>Marchantia polymorpha</i>: the absence of chloroplast-like tRNAs

Oda, Kazuhiro; Yamato, Katsuyuki T.; Ohta, Eiji; Nakamura, Yasukazu; Takemura, Masashi; Nozato, Naoko; Akashi, Kinya; Ohyama, Kanji

doi:10.1093/nar/20.14.3773

Cited by 46 publications

(24 citation statements)

References 23 publications

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“…We also identified native and cp-derived tRNA genes in six other plants, including one bryophyte ( M. polymorpha ) [51], one gymnosperm ( C. taitungensis ) [52], two monocots ( O. sativa and T. aestivum ), and two dicots ( A. thaliana and N. tabacum ) (Table 8) [53, 54]. Six cp-derived tRNA genes ( trnH-GUG , trnM-CAU , trnN-GUU , trnP-UGG , trnS-GGA , and trnW-CCA ) were common to the mt genomes of all angiosperms.…”

Section: Resultsmentioning

confidence: 99%

Analysis of the Complete Mitochondrial Genome Sequence of the Diploid CottonGossypium raimondiiby Comparative Genomics Approaches

Paterson

Wang

et al. 2016

BioMed Research International

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Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp) genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt) DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes. We also identified four larger repeats (63.9 kb, 10.6 kb, 9.1 kb, and 2.5 kb) in this mt genome, which may be active in intramolecular recombination in the evolution of cotton. Strikingly, nearly all of the G. raimondii mt genome has been transferred to nucleus on Chr1, and the transfer event must be very recent. Phylogenetic analysis reveals that G. raimondii, as a member of Malvaceae, is much closer to another cotton (G. barbadense) than other rosids, and the clade formed by two Gossypium species is sister to Brassicales. The G. raimondii mt genome may provide a crucial foundation for evolutionary analysis, molecular biology, and cytoplasmic male sterility in cotton and other higher plants.

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Section: Resultsmentioning

confidence: 99%

Analysis of the Complete Mitochondrial Genome Sequence of the Diploid CottonGossypium raimondiiby Comparative Genomics Approaches

Paterson

Wang

et al. 2016

BioMed Research International

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“…Compared with angiosperm and gymnosperm mitochondria, liverwort mitochondria contain the largest number of mtDNA-encoded tRNAs. However, even allowing for both G⅐U and U⅐N wobble base pairing, tRNAs reading the isoleucine codons AUU and AUC and the threonine codons ACA and ACG are still required (50). In both angiosperm and larch mitochondria, these tRNAs are imported, and nDNA-encoded tRNA AAU Ile and tRNA AGU Thr species have since been identified in liverwort mitochondria (51,52).…”

Section: Discussionmentioning

confidence: 99%

Identification and Structural Characterization of Nucleus-encoded Transfer RNAs Imported into Wheat Mitochondria

Glover

Spencer

Gray

2001

Journal of Biological Chemistry

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Despite its large size (200 -2400 kilobase pairs), the mitochondrial genome of angiosperms does not encode the minimal set of tRNAs required to support mitochondrial protein synthesis. Here we report the identification of cytosolic-like tRNAs in wheat mitochondria using a method involving quantitative hybridization to distinguish among three tRNA classes: (i) those encoded by mitochondrial DNA (mtDNA) and localized in mitochondria, (ii) those encoded by nuclear DNA and located in the cytosol, and (iii) those encoded by nuclear DNA and found in both the cytosol and mitochondria. The latter class comprises tRNA species that are considered to be imported into mitochondria to compensate for the deficiency of mtDNA-encoded tRNAs. In a comprehensive survey of the wheat mitochondrial tRNA population, we identified 14 such imported tRNAs, the structural characterization of which is presented here. These imported tRNAs complement 16 mtDNA-encoded tRNAs, for a total of at least 30 distinct tRNA species in wheat mitochondria. Considering differences in the set of mtDNA-encoded and imported tRNAs in the mitochondria of various land plants, the import system must be able to adapt relatively rapidly over evolutionary time with regard to the particular cytosolic-like tRNAs that are brought into mitochondria.

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“…in wheat (4,12). In M. polymorpha, the part encoding the C-terminal end of ccmF is further split in 2 genes (40). In Brasicacea such as Arabidopsis the part encoding the N-terminal end of ccmF is encoded by 2 genes (41,42).…”

Section: Ccmf In Mitochondrial Genomes-mentioning

confidence: 99%

The Three Mitochondrial Encoded CcmF Proteins Form a Complex That Interacts with CCMH and c-Type Apocytochromes in Arabidopsis

Rayapuram¹,

Hagenmuller²,

Grienenberger

et al. 2008

Journal of Biological Chemistry

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Three reading frames called ccmF N1 , ccmF N2 , and ccmF c are found in the mitochondrial genome of Arabidopsis. These sequences are similar to regions of the bacterial gene ccmF involved in cytochrome c maturation. ccmF genes are always absent from animal and fungi genomes but are found in mitochondrial genomes of land plant and several evolutionary distant eukaryotes. In Arabidopsis, ccmF N2 despite the absence of a classical initiation codon is not a pseudo gene. The 3 ccmF genes of Arabidopsis are expressed at the protein level. Their products are integral proteins of the mitochondrial inner membrane with in total 11 to 13 predicted transmembrane helices. The conserved WWD domain of CcmF N2 is localized in the inter membrane space. The 3 CcmF proteins are all detected in a high molecular mass complex of 500 kDa by Blue Native PAGE. Direct interaction between CcmF N2 and both CcmF N1 and CcmF C is shown with the yeast two-hybrid split ubiquitin system, but no interaction is observed between CcmF N1 and CcmF C . Similarly, interaction is detected between CcmF N2 and apocytochrome c but also with apocytochrome c 1 . Finally, CcmF N1 and CcmF N2 both interact with CCMH previously shown to interact as well with cytochrome c. This strengthens the hypothesis that CcmF and CCMH make a complex that performs the assembly of heme with c-type apocytochromes in plant mitochondria.

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Transfer RNA genes in the mitochondrial genome from a liverwort,Marchantia polymorpha: the absence of chloroplast-like tRNAs

Cited by 46 publications

References 23 publications

Analysis of the Complete Mitochondrial Genome Sequence of the Diploid CottonGossypium raimondiiby Comparative Genomics Approaches

Analysis of the Complete Mitochondrial Genome Sequence of the Diploid CottonGossypium raimondiiby Comparative Genomics Approaches

Identification and Structural Characterization of Nucleus-encoded Transfer RNAs Imported into Wheat Mitochondria

The Three Mitochondrial Encoded CcmF Proteins Form a Complex That Interacts with CCMH and c-Type Apocytochromes in Arabidopsis

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