Naoko Nozato

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA: A primitive form of plant mitochondrial genome

Analysis of the mitochondrial DNA of a liverwort Marchantia polymorpha by electron microscopy and restriction endonuclease mapping indicated that the liverwort mitochondrial genome was a single circular molecule of about 184,400 base-pairs. We have determined the complete sequence of the liverwort mitochondrial DNA and detected 94 possible genes in the sequence of 186,608 base-pairs. These included genes for three species of ribosomal RNA, 29 genes for 27 species of transfer RNA and 30 open reading frames (ORFs) for functionally known proteins (16 ribosomal proteins, 3 subunits of H(+)-ATPase, 3 subunits of cytochrome c oxidase, apocytochrome b protein and 7 subunits of NADH ubiquinone oxidoreductase). Three ORFs showed similarity to ORFs of unknown function in the mitochondrial genomes of other organisms. Furthermore, 29 ORFs were predicted as possible genes by using the index of G + C content in first, second and third letters of codons (42.0 +/- 10.9%, 37.0 +/- 13.2% and 26.4 +/- 9.4%, respectively) obtained from the codon usages of identified liverwort genes. To date, 32 introns belonging to either group I or group II intron have been found in the coding regions of 17 genes including ribosomal RNA genes (rrn18 and rrn26), a transfer RNA gene (trnS) and a pseudogene (psi nad7). RNA editing was apparently lacking in liverwort mitochondria since the nucleotide sequences of the liverwort mitochondrial DNA were well-conserved at the DNA level.

Complete nucleotide sequence of the mitochondrial DNA from a liverwort,Marchantia polymorpha

Libraries of cosmid and plasmid clones covering the entire region of mtDNA from the liverwortMarchantia polymorpha were constructed. These clones were used for the determination of the complete nucleotide sequence of the liverwort mtDNA totally 186,608 bp (GenBank no. M68929) and including genes for 3 species of ribosomal RNAs, 29 genes for 27 species of transfer RNAs, and 30 genes for functionally known proteins (16 ribosomal proteins, 3 subunits of cytochromec oxidase, apocytochromeb protein, 3 subunits of H+-ATPase, and 7 subunits of NADH ubiquinone oxidoreductase). The genome also contains 32 unidentified open reading frames. Thus the complete nucleotide sequences from both chloroplast and mitochondrial genomes have been determined in the same organism. Plasmid clones are available upon the request.

Active transcription of the pseudogene for subunit 7 of the NADH dehydrogenase in Marchantia polymorpha mitochondria

A pseudogene, ψnad7, which has significant sequence similarity (66.7% amino acid identity) with the bovine nuclear gene for a 49 kDa subunit of the NADH dehydrogenase (NADH:ubiquinone oxidoreductase, EC 1.6.99.3), has been identified on the mitochondrial genome of the liverwort Marchantia polymorpha. The predicted coding region, which includes six termination codons, is actively transcribed into RNA molecules of 16 and 9.6 kb in length, but RNA splicing products were not detected in the liverwort mitochondria. Genomic DNA blot analysis and RNA blot analysis using poly(A)+ RNA suggest that a structurally related nuclear gene encodes the mitochondrial ND7 polypeptide. These results imply that this ψnad7 is a relic of a gene transfer event from the mitochondrial genome into the nuclear genome during mitochondrial evolution in M. polymorpha.

Cotranscriptional expression of mitochondrial genes for subunits of NADH, dehydrogenase, nad5, nad4, nad2, in Marchantia polymorpha

SummaryThree genes for the subunits of the NADH dehydrogenase (nad5, nad4, and nad2) are tandemly clustered on the liverwort mitochondrial genome. Their gene products showed high levels of amino acid sequence identity with the corresponding subunits from higher plant mitochondria (82.8–84.4%), and significant levels of identity with those from liverwort chloroplast (32.0–33.5%), Podospora anserina mitochondria (21.4–45.9%), and human mitochondria (18.4–27.9%). In addition, these three subunits from liverwort mitochondria have conserved amino acid residues in their central regions. The gene nad5 is interrupted by a 672 by group I intron, while genes nad4 and nad2 are interrupted by group II introns of 899 by and 1418 bp, respectively. Northern blot analysis using exon-intron specific probes indicated that these three genes are transcribed as a single precursor mRNA of 9.6 kb in length and are processed into mature mRNA molecules in liverwort mitochondria. Several regions of this nad gene cluster are repeated in the liverwort mitochondrial genome.

Distribution and forms of selenium in paddy soil

Abstract Distribution and forms of selenium (Se) in paddy soil profiles were investigated. Data on the total Se content indicated that there was a distinct accumulation of Se in the B horizons, and that the content of Se was higher in the C horizons than in the A horizons. A significant difference in Se species between the upper and lower horizons was recognized. Since the amount of Se compounds with low molecular weight such as inorganic Se and Se bound with fulvic acids increased significantly in the lower horizons as compared to the upper horizons, it was assumed that Se was translocated in these soil profiles. Two mechanisms for the movement may be considered: (1) Inorganic Se released upon dissolution of iron oxides and iron hydroxides was translocated with percolating water. (2) Se compounds contained in fulvic acids were translocated with the movement of fulvic acids. In 6 out of 7 profiles, Se may have moved according to the first mechanism, whereas in the other one, both mechanisms may have been ...

Occurrence and transcription of genes for nad1, nad3, nad4L, and nad6, coding for NADH dehydrogenase subunits 1, 3, 4L, and 6, in liverwort mitochondria

The genes encoding subunits 1, 3, 4L, and 6 of NADH dehydrogenase (nad1, nad3, nad4L, nad6) in the mitochondrial genome of a liverwort, Marchantia polymorpha, were characterized by comparing homologies of the amino-acid sequences of the subunits with those of other organisms. The nad3 and nad4L genes are split by single and double group II introns, respectively. The 5′-half portion of the nad6 gene was repeated at an identity of 89% to form a reading frame consisting of 100 amino-acid residues. The Northern hybridization analysis showed that all four genes are transcribed in the liverwort mitochondria.

Evolution of Organellar Genomes

In the plant kingdom, the endosymbiotic event of a mitochondrial ancestor probably happened first to plant cell progenitors followed by the endosymbiosis of a chloroplast ancestor, namely cyanobacteria. In this paper we describe the characterization of plant mitochondrial genome focussing on (1) the complexity of plant mitochondrial genomes, (2) the genetic codes utilized in plant mitochondrial genomes, (3) the properties of open reading frames encoded by introns (group I and group II) of plant mitochondrial genes, and (4) RNA editing which has been reported in wheat mitochondrial genome (C to U conversion), and (5) evolutionary events of gene migration from mitochondrial and chloroplast genomes to nuclear genomes.