Origin of the S-1 plasmid-like DNA molecule of maize mitochondria

The mitochondria of certain maize cytoplasms contain linear plasmid-like DNAs in addition to the main mitochondrial genome. The male-sterile cytoplasm, cms-S, has two plasmid-like DNA molecules. These are designated S-1 and S-2 and are 6.4 kilobases (kb) and 5.4 kb long, respectively. A few male-fertile South American maize races, such as Racimo de Uva, also contain two plasmid-like DNA molecules, R-1 and R-2, which are 7.5 kb and 5.4 kb long, respectively. Restriction mapping and heteroduplexing studies reveal that R-2 and S-2 are nearly identical. In contrast, S-1 contains regions of homology with R-1 and R-2. It has been suggested that S-1 may have arisen from a recombinational event between R-1 and R-2 (Figure 1) (see review in Plant Gene Research, Ch. 6, B. Hohn and E. S. Dennis, Ed., Springer-Verlag, New York).

To investigate this possibility, a 458 base pair (bp) HindIII-BamHI fragment, believed to contain the site of recombination, was isolated from R-1 (Racimo de Uva) and sequenced using the dideoxynucleotide chain termination protocol. This sequence was compared with the sequences of S-1 (EMBO J., 4:1125, 1985) and S-2 (Proc. Natl. Acad. Sci. USA, 80:4055, 1983). The comparisons show well defined regions of sequence homology and nonhomology that indicate the probable point of recombination (Figure 2).

The probable point of recombination occurs between bases 4935 and 4936 in S-1, bases 3991 and 3992 in S-2, and bases 412 and 413 in R-1 (Figure 2). Because S-2 and R-2 are virtually identical, S-2 was used for comparison.

There are no large open reading frames (ORFs) in this segment of S-2, but the HindIII-BamHI R-1 and corresponding S-1 strand contain a large unidentified reading frame (URF) that continues through the recombination point and beyond the HindIII site. This URF is homologous with the 768 bp URF-4 in S-1 (EMBO J., 4:1125, 1985). A search of BIONET protein libraries has revealed no significant homologies. Finally, we believe our results support the view that S-1 arose by a recombination between R-1 and R-2.

Figure 1. Homologies between the various plasmid-like DNAs. Vertical lines indicate probable recombination point. Curved arrow illustrates recombination event and straight arrow illustrates the resulting S-1 hybrid.

Figure 2. Sequence comparison of R-1, S-1, and S-2 presented in a 5' to 3' direction. Arrows indicate point of recombination. The R-1 sequence from nucleotide 1 to 412 has perfect homology with the S-1 sequence from nucleotide 4864 to 4935 (not all data shown); beyond that point R-1 and S-1 have no significant homology. S-1 has nearly perfect homology with S-2 beginning at nucleotide 4936 in S-1 and 3992 in S-2, continuing to their 3' termini. Prior to that point, S-1 and S-2 do not contain significant homology (not all data shown). S-1 and S-2 vary from each other at positions 4963,4964 and 4019,4020, respectively, in the homologous region.

Susan Elmore-Stamper and C. S. Levings III

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

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