Curt Genet (1988)13:83-89 Current Genetics © Springer-Vedag 1988 Chimeric organization of two genes for the soybean mitochondrial ATPase subunit 6 Elizabeth Grabau*, Marie Havlik, and Raymond Gesteland Howard Hughes Medical Institute, Universityof Utah, Salt Lake City, UT 84132, USA Summary. There are two copies of the ATPase subunit 6 (atp6) gene in the soybean mitochondrial genome which differ in their gene organization but share extensive homology with the maize atp6 gene except at their 5' ends. The two soybean genes are chimeric, containing regions with homology to other known mitochondrial • genes at their 5' ends. Sequences homologous to the cytochrome oxidase subunit II (coxlI) are located in one copy and sequences homologous to the ATPase subunit 9 (atp9) gene are located in the other copy, both of which contain methionine (ATG) codons that are in-frame with the remainder of the atp6 open reading frame. At least the copy of atp6 that contains the coxlI sequence at its 5' end is abundantly transcribed to give an RNA of approximately 1,200 nucleotides. Key words: Plant mitochondria - Glycine max - ATP- ase - Chimeric gene Introduction The ATPase enzyme complex of mitochondria consists of subunits encoded by both mitochondrial and nuclear genes. In plants at least subunits 6 and 9 (Dewey et al. 1985a; Dewey et al. 1985b; Bland et al. 1986; Young et al. 1986) and alpha (Braun and Levings 1985; Isaac et al. 1985) are mitochondrially-encoded. Sequences of the atp6 gene seem unusual in that they have been found in conjunction with rearrangements of plant mitochondrial DNA (Dewey et al. 1985a; Dewey et al. Present address: Department of Agronomyand Plant Genetics, Borlaug Hall, Universityof Minnesota, St. Paul, MN 55108, USA Offprint requests to: E. Grabau 1986). The single maize atp6 gene has been identified by homology to yeast atp6 (Dewey et al. 1985a) and sequencing has revealed three possible ATG initiation codons with the second favored by homology arguments. A 122 nucleotide internal portion of the coding region of this gene is also found adjacent to the maize coxII gene just upstream from its putative ATG initiation codon. This juxtaposition has not been found in the other plant coxII genes sequenced to date (Grabau 1987; Bonen et al. 1984; Kao et al. 1984; Hiesel and Brennicke 1983; Moon et al. 1985). A portion of the 5' flanking sequence of maize atp6 (-1,589 to -445 with respect to the initiation codon) is also found within a region of mitochondrial DNA that is unique to the maize T-type cytoplasmic male sterile line (cresT) designated TURF 2H3 (Dewey et al. 1986). TURF 2H3 also contains sequences homologous to the 26S ribosomal RNA gene and to the tobacco chloroplast tRNA Arg gene. The sequence of the TURF 2H3 region shows the presence of two open reading frames and this region is transcribed. One of the open reading frames is unique to cmsT and could encode a protein with a pre- dicted molecular weight of 13,000. It is postulated that at least seven recombinational events occurred to produce this chimeric region. The coxII gene of wheat mitochon- dria represents another example where a fragment of a gene is located elsewhere in the mitochondrial genome (Bonen et al. 1984). A 193 nucleotide sequence corres- ponding to the transmembrane domain of wheat coxII is present at a second location. In characterizing the atp6 gene from the soybean mitochondrial genome, we found two copies of the gene that differ from the single maize gene by having DNA sequences homologous to either coxII or atp9 at their 5' ends. Their sequences reveal that in both cases the chimeric 5' ends are aligned with the remainder of the atp6 coding sequence and contain ATG codons which