Genetic and physical maps and a clone bank of mitochondrial DNA from rice

The rice mitochondrial genomes and their variations

Based on highly redundant and high-quality sequences, we assembled rice (Oryza sativa) mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S (an indica-like variety with maternal origin of japonica), which are paternal and maternal strains of an elite superhybrid rice Liang-You-Pei-Jiu (LYP-9), respectively. Following up with a previous analysis on rice chloroplast genomes, we divided mitochondrial sequence variations into two basic categories, intravarietal and intersubspecific. Intravarietal polymorphisms are variations within mitochondrial genomes of an individual variety. Intersubspecific polymorphisms are variations between subspecies among their major genotypes. In this study, we identified 96 single nucleotide polymorphisms (SNPs), 25 indels, and three segmental sequence variations as intersubspecific polymorphisms. A signature sequence fragment unique to indica varieties was confirmed experimentally and found in two wild rice samples, but absent in japonica varieties. The intersubspecific polymorphism rate for mitochondrial genomes is 0.02% for SNPs and 0.006% for indels, nearly 2.5 and 3 times lower than that of their chloroplast counterparts and 21 and 38 times lower than corresponding rates of the rice nuclear genome, respectively. The intravarietal polymorphism rates among analyzed mitochondrial genomes, such as 93-11 and PA64S, are 1.26% and 1.38% for SNPs and 1.13% and 1.09% for indels, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago.

A ribosomal protein L2 gene is transcribed, spliced, and edited at one site in rice mitochondria

The mitochondrial ribosomal protein L2 gene (rpl2) is coded by two exons of 840 and 669 bp separated by an intron sequence of 1481 bp in the rice mitochondrial genome. The rpl2 gene is located three nucleotides upstream of the ribosomal protein S19 gene (rps19) and both genes are co-transcribed. cDNA sequence analysis identified splicing of the intron sequence from the rpl2 mRNA as well as RNA editing events. The deduced secondary structure of the rpl2 intron sequence shows the characteristic features of a group-II intron. A single RNA editing site is identified in rpl2 and six editing sites in rps19 transcripts. In addition, one editing site is observed in the 3 nucleotide intergenic region. Analysis of individual cDNA clones showed a different extent of RNA editing. The rice rpl2 intron is located at a different site and shows no significant nucleotide sequence similarity with the rpl2 intron of liverwort. However, 60% nucleotide sequence identity is observed between the rice rpl2 intron and the Oenothera nad5 intron in a 234 nucleotide region. The mitochondrial rpl2 sequence is absent from the pea mitochondrial genome and we consequently propose that the mitochondrial RPL2 protein is encoded by a nuclear gene in pea.

Multiple initiation sites for transcription of a gene for subunit 1 of F1-ATPase (atp1) in rice mitochondria

We identified the sites for the initiation of transcription of a gene for subunit 1 of F1-ATPase (atp1) in rice mitochondrial DNA. Capping and ribonuclease protection experiments in vitro, together with primer extension analysis, demonstrated that there were at least eight transcription initiation sites upstream of atp1. One initiation site, expressed most actively, was flanked by a sequence identical to the consensus promotor motif of rice mitochondrial genes. However, the sequences surrounding the other seven initiation sites exhibited no similarity to the consensus sequence.

The gene for a subunit of an ABC-type heme transporter is transcribed together with the gene for subunit 6 of NADH dehydrogenase in rice mitochondria

We previously identified a chloroplast-derived (ct-derived) sequence of 32 base pairs (bp) in rice mitochondrial DNA that includes a part (30 bp; psitrnI) of a gene for isoleucine tRNA (CAU) of the chloroplast. Analyzing the ct-derived psitrnI, we found that an open reading frame (orf240), which was homologous to the gene for a subunit of an ATP-binding cassette-type (ABC-type) heme transporter, namely helC, of Rhodobacter capsulatus, and a gene for subunit 6 of NADH dehydrogenase (nad6) were located upstream of and downstream from the ct-derived psitrnI, respectively. Northern-blot hybridization and analysis by reverse transcription-polymerase chain reaction (RT-PCR) revealed that both orf240 and nad6 were co-transcribed in rice mitochondria. An analysis of PCR-amplified fragments of the region of orf240/nad6 from the DNA of some Gramineae suggests that the arrangement of orf240/nad6 was generated in the mitochondrial genome of the genus Oryza during evolution after its divergence from the other Gramineae. Most of the transcripts of orf240 are edited, with a change from cytidine to uridine, at 35 positions. Editing of the RNA changes 33 amino-acid residues among the 240 encoded amino-acid residues, suggesting that the orf240 gene is functional in rice mitochondria.

High-frequency inter-parental recombination between mitochondrial genomes of rice cybrids

Analyzing more than 100 independent rice cybrids, we found evidence for inter-molecular recombination between parental mitochondrial genomes occurring at high frequency soon after protoplast fusion. The structure of the region around the atp6 gene showed extensive polymorphism among Indica (MTC-5A), Japonica (Nipponbare), and wild abortive (IR58024A) mitochondrial genomes. Recombination between the mitochondrial genomes of IR58024A and MTC-5A around the atp6 gene was detected by Southern-blot analysis of cybrid plants. Such recombinant mitochondrial molecules were also cloned from IR58024A/Nipponbare cybrid callus. PCR analysis around the atp6 gene demonstrated that inter-parental recombination occurs in practically all cybrid calli within 2 weeks after protoplast fusion. At this point, parental and recombinant mitochondrial genomes co-existed within the callus. Over the course of further cultivation, however, mitochondrial genome diversity decreased as parental and/or recombinant genomes segregated out.

The genes encoding subunit 3 of NADH dehydrogenase and ribosomal protein S12 are co-transcribed and edited in Pinus sylvestris (L.) mitochondria

The nucleotide sequence of the region encoding NADH dehydrogenase subunit 3 and ribosomal protein S12 from Pinus sylvestris (L.) mitochondrial DNA (mtDNA) has been determined. A sequence comparison of this region with six individual cDNA clones prepared by RT-PCR revealed 35 C-to-T differences, showing the occurrence of RNA editing. All but one of these alterations in mRNA sequence change codon identities to specify amino acid better conserved in evolution. Most of these modifications take place within the nad3 gene changing 20% of the amino-acid sequence, which is much more than in angiosperms. Of six cDNA clones investigated, four clones of nad3 were differentially edited, but the editing of the rps12 sequences was identical. As in angiosperms, the two genes are separated by a short sequence of 52 bp, which is not edited. Two transcripts of about 0.9 kb and 1.2 kb, each encoding both proteins, have been detected by Northern hybridisation. The hybridisation of nad3 and rps12 probes with pine mtDNA digested with different restriction enzymes indicates that both genes are present in a single copy in pine mtDNA. The analysis of PCR amplification products with gene-specific primers shows a conserved order of these genes in a wide range of gymnosperms.

Organization of the mitochondrial Cob 2 pseudogene in different lines of rice

In the fertile rice line IR 36 there are two copies of the apocytochrome b (cob) gene: a functional copy, cob 1, and a pseudogene, cob 2 (Kaleikau et al. 1992). In a survey of diverse rice lines, we found that cob 2 was absent in the wild abortive(WA)-type cytoplasmic male-sterile cytoplasm, but was present in the fertile lines. While cob 1 was conserved among all the lines, fertile and sterile, the cob 2 region was different in the fertile lines tested. The 5' regions of most cob 2 loci were similar to cob 1 (about 4 kb of the flanking region and most of the coding region), but the 3' region varied among different fertile lines. The point of divergence, the break-point, from the cob 1 sequence was conserved in all the cob 2 regions tested. In all the cob 2 regions, this break-point seems to be linked to the variable region of cob 2 through a conserved 192-bp segment, which is not a part of cob 1. It is proposed that the cob 2 regions could have been produced by recombination or insertion events involving cob 1 and the 192-bp segment which is present at different locations in the mitochondrial genomes of the various rice lines.

A small repeated sequence contains the transcription initiation sites for both trnfM and rrn26 in rice mitochondria

The 76 bp sequence found in the upstream region of a gene for 26S rRNA (rrn26) is duplicated in the upstream region of a gene for initiator methionine tRNA (trnfM) in the mitochondrial genome of rice. An in vitro capping/ribonuclease protection assay and primer extension analysis demonstrated that the transcription of trnfM and of rrn26, which are at least 190 kb from one another in the rice mitochondrial genome, starts from these same sequences in the upstream regions of the respective genes. This result indicates that the short sequence that is duplicated in the upstream regions of trnfM and rrn26 in rice mtDNA is recognized as the promoter of each respective gene.

Evolutionary variations in DNA sequences transferred from chloroplast genomes to mitochondrial genomes in the Gramineae

The transfer of fragments of DNA from chloroplast genomes to mitochondrial genomes is considered to be a general phenomenon in higher plants. In the present study, Southern hybridization, together with amplification by PCR and DNA sequencing techniques, was used to examine the regions homologous to chloroplast rps19 in the mitochondrial genomes of several gramineous plants. In all the mitochondrial DNAs from the gramineous plants examined, except for that from wheat, the transferred fragments of chloroplast DNA were found to be maintained and the same junctions of mitochondrion-specific and chloroplast-like sequences were found at one terminus. This finding indicates that the transfer of the chloroplast sequence occurred in the distant past during the evolution of gramineous plants. Subsequent analysis revealed that the fragments had been variously rearranged among species with respect to the other terminus. Considering the current diversity of this one particular transferred fragment of chloroplast DNA, we propose that chloroplast-derived DNA sequences that have lost their original functions tend to be rearranged during evolution in mitochondrial genomes.

A unique sequence located downstream from the rice mitochondrial atp6 may cause male sterility

Asymmetric cell-fusion of the japonica cultivar of Oryza sativa (rice) with cytoplasmic-male-sterile (CMS) plants bearing cytoplasm derived from Chinsurah Boro II, resulted in two classes of cytoplasmic hybrids (cybrids), fertile and CMS. Southern-blot analysis of the mitochondrial DNA (mtDNA) indicates recombination events around a number of genes; however, the appearance of the CMS character is tightly correlated to reorganization around the atp6 gene, suggesting recombination downstream from the atp6 gene is involved in CMS. The nucleotide sequence downstream from atp6 contains a pseudogene which was probably created by recombination of the mitochondrial genome. Sense and antisense transcripts of the downstream region of atp6 were found in CMS- and restored CMS (fertile)-lines, but not in the normal (fertile) line. In the CMS line, several antisense transcripts of the atp6 gene were also found. However, in the restored line which contains a nuclear-encoded gene, Rf-1, the levels of these transcripts were lower than in the CMS line. These results suggest abnormal transcripts of the atp6 gene produced in the antisense direction may be involved in CMS, and that products of the nuclear-encoded restorer gene may reduce abnormal transcription in this region of the mitochondrial genome.

Palindromic repeated sequences (PRSs) in the mitochondrial genome of rice: evidence for their insertion after divergence of the genus Oryza from the other Gramineae

We have identified a family of small repeated sequences (from 60 to 66 bp in length) in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare). There are at least ten copies of these sequences and they are distributed throughout the mitochondrial genome. Each is potentially capable of forming a stem-and-loop structure and we have designated them PRSs (palindromic repeated sequences). Their features are reminiscent of the small dispersed repeats in the mitochondrial DNA (mtDNA) of some lower eukaryotes, such as Saccharomyces cerevisiae, Neurospora crassa and Chlamydomonas reinhardtii. Some of the PRSs of rice mtDNA are located in the intron of the gene for ribosomal protein S3 (rps3) and in the flanking sequence of the gene for chloroplast-like tRNA(Asn) (trnN). analysis of PCR-amplified fragments of these regions from the DNA of some Gramineae suggests that the PRSs were inserted into these regions of the Oryza mtDNA after the divergence of Oryza from the other Gramineae.

Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice

The entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare) was identified using clone banks that cover the chloroplast and mitochondrial genomes. The mitochondrial fragments that were homologous to chloroplast DNA were mapped and sequenced. The nucleotide sequences around the termini of integrated chloroplast sequences in the rice mtDNA revealed no common sequences or structures that might enhance the transfer of DNA. Sixteen chloroplast sequences, ranging from 32 bases to 6.8 kb in length, were found to be dispersed throughout the rice mitochondrial genome. The total length of these sequences is equal to approximately 6% (22 kb) of the rice mitochondrial genome and to 19% of the chloroplast genome. The transfer of segments of chloroplast DNA seems to have occurred at different times, both before and after the divergence of rice and maize. The mitochondrial genome appears to have been rearranged after the transfer of chloroplast sequences as a result of recombination at these sequences. The rice mitochondrial DNA contains nine intact tRNA genes and three tRNA pseudogenes derived from the chloroplast genome.