Some physicochemical properties of rice mitochondrial DNA

Electron microscopic investigation of mitochondrial DNA from Chenopodium album (L.)

DNA molecules from mitochondria of whole plants and a suspension culture of Chenopodium album were prepared, by a gentle method, for analysis by electron microscopy. Mitochondrial (mt) DNA preparations from both sources contained mostly linear molecules of variable sizes (with the majority of molecules ranging from 40 to 160 kb). Open circular molecules with contour lengths corresponding to 0. 3-183 kb represented 23-26% of all mtDNA molecules in the preparations from the suspension culture and 13-15% in the preparations from whole plants. More than 90% of the circular DNA was smaller than 30 kb. Virtually no size classes of the mtDNA molecules could be identified, and circular or linear molecules of the genome size (about 270 kb) were not observed. In contrast, plastid (pt) DNA preparations from the suspension culture contained linear and circular molecules falling into size classes corresponding to monomers, dimers and trimers of the chromosome. About 23% of the ptDNA molecules were circular. DNA preparations from mitochondria contained a higher percentage of more complex molecules (rosette-like structures, catenate-like molecules) than preparations of ptDNA. Sigma-like molecules (putative intermediates of rolling-circle replication) were observed in mtDNA preparations from the suspension culture (18% of the circles), and in much lower amount (1%) in preparations from whole plants. The results are compared with data obtained previously by pulsed-field gel electrophoresis and discussed in relation to the structural organization and replication of the mt genome of higher plants.

Organization of a 117-kb circular mitochondrial chromosome in IR36 rice

The organization of the mitochondrial genome in the IR36 indica variety of rice was analyzed using constant-field and CHEF gel electrophoresis. The minimum complexity of the genome is estimated to be 300 kb. There was no evidence for a master circular molecule of this size. The genome exists in vivo in multiple subgenomic circular molecules or mitochondrial chromosomes. Using several rare-cutting restriction enzymes a restriction map was constructed for a 117-kb circular chromosome. Six genetic loci have been placed on this chromosome; cox1 and atp1 have been assigned precise positions while four additional genes (rrn26, cob2, atp6 and rrn18) were mapped to restriction fragments.

A repeated chromosomal DNA sequence is amplified as a circular extrachromosomal molecule in rice (Oryza sativa L.)

The plasmid pE10 is a pBR322-derived plasmid carrying a 4.5 kb rice (Oryza sativa L.) repeated DNA sequence. The cloned sequence has been shown to be amplified in cultured rice cells. The analysis of practically intact chromosomal rice DNA molecules by pulsed field gel electrophoresis has now shown that the amplification is associated with the appearance of extrachromosomal molecules. In fact, pE10 hybridizes exclusively with unfractionated DNA from leaf protoplasts, while it recognizes predominantly an extrachromosomal DNA molecule (ECD) of about 45 kb and its multiples in the case of protoplasts from cultured cells. Insensitivity to the action of the exonuclease Bal31 suggests that the molecule is circular. Analysis of restriction endonuclease products with both standard horizontal and pulsed field gel electrophoresis suggest that the extrachromosomal DNA, and its chromosomal counterpart, is composed of tandemly repeated units of about 7 kb. Thus, the smaller extrachromosomal circle should contain 6-7 repeats, while the sequence cloned in pE10 is a subset of this repeat. The extrachromosomal DNA represents about 1% of total rice DNA and its level of amplification is not affected by the different phases of growth in culture.

Stability of mitochondrial DNA in tissue-cultured cells of rice

Restriction analysis of mitochondrial (mt) DNA from 3-month-old callus cultures of the cytoplasmic male sterile rice, V41A, which contains S2 or "wild abortive" cytoplasm, and its fertile maintainer, V41B, showed the same BamHI restriction profiles as mtDNA from the corresponding leaf material. Similarly, mtDNA of rice (var. Taipei 309) from leaves, a 2-month-old cell suspension (T3MS2/A), a totipotent suspension (T3MS) and a 19-month-old suspension, which had lost its protoplast regeneration ability (LB3), showed indistinguishable BamHI restriction profiles. However, clear differences in mtDNA restriction profiles were observed between LB3 and a 30-month-old suspension culture of Taipei 309 (LB1), which appeared to reflect substantial changes in the relative abundance of specific DNA sequences. Hybridisation of a maizecoxII gene probe to blots of restricted mtDNA confirmed that, while the relative abundance of certain mtDNA sequences was preserved during long-term tissue culture of rice, major changes in abundance were observed with other sequences.

Double-stranded RNA and male sterility in rice

Double-stranded RNA (dsRNA) was isolated from rice Oryza sativa ssp. japonica, but not from other subspecies. The dsRNA has been found in all of the examined cytoplasmic male-sterile (CMS) lines of BT (Chinsurah Boro II)-type rice, but was not detected in their companionate maintainer lines. It is uniquely and positivley correlated with the CMS trait in BT-type rice. Recently, the dsRNA was also found in a nuclear malesterile (NMS) rice, Nongken 58s, but was not found in its normal Nongken 58. The molecular weight of this dsRNA was estimated to be about 18 kb. Electron microscopic analysis reveals that it is linear snapped. The double strandedness of the RNA molecules was characterized by CF-11 cellulose column chromatography and nuclease treatments. It bound to CF-11 cellulose in the presence of 15% ethanol. It was sensitive to RNase A at low salt concentrations, but insensitive to DNase I, SI nuclease, and RNase A at high salt concentrations. The dsRNA was detected in both mitochondrial and cytoplasmic fractions. Dot-blot hybridization reveals that there is no sequence homology between this dsRNA and mtDNA, but there is homology between this dsRNA and nuclear genomic DNA. We have not been able to transmit this dsRNA to fertile rice.