Abstract
Identification of the soybean mitochondrial atpA open reading frame (atpA ORF) was based on sequence similarity with atpA genes in other plant mitochondria and partial protein sequencing. The atpA reading frame ends with four tandem UGA codons which overlap four tandem AUG codons initiating an unidentified reading frame, orf214. The atpA-orf214 region is found in multiple sequence contexts in soybean mitochondrial DNA (mtDNA), which can be attributed to the presence of two recombination repeats. A 1-kb repeat spans 600 nucleotides (nt) of atpA N-terminal coding region and 400 nt of upstream sequence. Its four configurations correspond to two full-length atpA-orf214 genes and two truncated pseudogenes. A 2-kb repeat lies 3 kb downstream from the 1-kb repeat. Restriction maps of cosmid clones suggest that a 10-kb segment containing both repeats is itself duplicated in the mt genome. With two recombination repeats present in a total of three copies per genome, soybean mtDNA is expected to consist of a complex population of subgenomic molecules. Transcription of the atpA loci was analysed by Northern blotting and S1 nuclease protection. The atpA genes express multiple transcripts with one major 3′ end and heterogeneous 5′ sequences extending several kb upstream of the atpA coding region. The atpA gene and orf214 are co-transcribed on all major transcripts. The pseudogenes do not express stable RNAs.
Similar content being viewed by others
References
Aebersold RH, Teplow DB, Hood LE, Kent SBH (1986) J Biol Chem 261:4429–4438
Bailey-Serres J, Hanson DK, Fox TD, Leaver CJ (1986) Cell 47:567–576
Bailey-Serres J, Leroy P, Jones SS, Wahleithner JA, Wolstenholme DR (1987) Curr Genet 12:49–53
Bendich AJ (1985) Plant mitochondrial DNA: unusual variation on a common theme. In: Hohn B, Dennis ES (eds) Plant gene Research, vol 2. Springer-Verlag, Vienna, pp 111–138
Bendich AJ, Smith SB (1990) Curr Genet 17:421–425
Bégu D, Graves P-V, Domec C, Arselin G, Litvak S, Araya A (1990) Plant Cell 2:1283–1290
Bland MM, Levings CS III, Matzinger DF (1986) Mol Gen Genet 204:6–16
Braun CJ, Levings CSIII (1985) Plant Physiol 79:571–577
Brears T, Lonsdale DM (1988) Mol Gen Genet 214:514–522
Chase CD, Ortega VM (1992) Curr Genet 22:147–153
Chaumont F, Boutry M, Briquet M, Vassarotti A (1988) Nucleic Acids Res 16:6247
Church GM, Gilbert W (1984) Proc Natl Acad Sci USA 81:1991–1995
Church GM, Kieffer-Higgins S (1988) Science 240:185–188
Covello PS, Gray MW (1989) Nature 341:662–666
Dawson AJ, Jones VP, Leaver CJ (1984) EMBO J 3:2107–2113
Dewey RE, Levings CS III; Timothy DH (1986) Cell 44:439–449
Finnegan PM, Brown GG (1990) Plant Cell 2:71–83
Folkerts O, Hanson MR (1989) Nucleic Acids Res 17:7341–7357
Grabau EA (1985) Plant Mol Biol 5:119–124
Grabau EA, Havlik M, Gesteland RF (1988) Curr Genet 13:83–89
Gualberto JM, Lamattina L, Bonnard G, Weil J-H, Grienenberger J-M (1989) Nature 341:660–662
Handa H, Nakajima K (1991) Plant Mol Biol 16:361–364
Hiesel R, Wissinger B, Schuster W, Brennicke A (1989) Science 246:1632–1634
Isaac GI, Brennicke A, Dunbar M, Leaver CJ (1985) Curr Genet 10:321–328
Kadowaki K, Kazama S, Suzuki S (1990) Nucleic Acids Res 18:1302
Keim P, Olson TC, Shoemaker RC (1988) Soybean Genet Newslett 5:150–152
Köhler RH, Lössl A, Zetsche K (1990) Nucleic Acids Res 18:4588
Krebbers ET, Larrinua IM, McIntosh L, Bogorad L (1982) Nucleic Acids Res 10:4985–5002
Leaver CJ, Isaac PG, Small ID, Bailey-Serres J, Lidell AD, Hawkesford MJ (1988) Phil Trans R Soc Lond 319:165–178
Levings CSIII, Pring DR (1979). Mitochondrial DNA of higher plants and genetic engineering. In: Setlow JK, Hollaender A (eds) Genetic engineering, vol 1. Plenum Press, New York, pp 205–222
Lonsdale DM, Hodge TP, Fauron CM-R (1984) Nucleic Acids Res 12:9249–9261
MacFarlane JL, Wahleithner JA, Wolstenholme DR (1990) Curr Genet 17:33–40
Makaroff CA, Apel IJ, Palmer JD (1990) Plant Mol Biol 15:735–746
Morgens PH, Grabau EA, Gesteland RF (1984) Nucleic Acids Res 12:5665–5683
Morikami A, Nakamura K (1987) J Biochem 101:967–976
Mulligan RM, Lau GT, Walbot V (1988a) Proc Natl Acad Sci USA 85:7998–8002
Mulligan RM, Maloney AP, Walbot V (1988b) Mol Gen Genet 211:373–380
Mulligan RM, Leon P, Walbot V (1991) Mol Cell Biol 11:533–543
Newton KJ, Knudsen C, Gabay-Laughnan S, Laughnan JR (1990) Plant Cell 2:107–113
Nugent JM, Palmer JD (1991) Cell 66:473–481
Palmer JD (1988) Genetics 118:341–351
Palmer JD, Herbon LA (1986) Nucleic Acids Res 14:9755–9764
Palmer JD, Herbon LA (1987) Curr Genet 11:565–570
Palmer JD, Shields CR (1984) Nature 307:437–440
Rothenberg M, Hanson MR (1988) Genetics 118:155–161
Sambrook J, Fritsch EF, Maniatis T (1989) In: Ford N, Nolan C, Ferguson M (eds) Molecular cloning: a laboratory manual. Cold-Spring Harbor Laboratory, Cold Spring Harbor, New York
Sanger F, Nicklen S, Coulson AR (1977) Proc Natl Acad Sci USA 74:5463–5467
Schulte E, Staubach S, Laser B, Kück U (1989) Nucleic Acids Res 17:7531
Schuster W, Brennicke A (1986) Mol Gen Genet 201:29–35
Schuster W, Hiesel R, Isaac PG, Leaver CJ, Brennicke A (1987) Nucleic Acids Res 14:5939–5954
Siculella L, D'Ambrosio L, De Tuglie AD, Gallerani R (1990) Nucleic Acids Res 18:4599
Sparks RB, Dale RMK (1980) Mol Gen Genet 180:351–355
Stern DB, Newton KJ (1986) Methods Enzymol 118:488–496
Stern DB, Palmer JD (1984) Nucleic Acid Res 12:6141–6157
Stern DB, Palmer JD (1986) Nucleic Acids Res 14:5651–5666
Synenki RM, Levings CSIII, Shah DM (1978) Plant Physiol 61:460–464
Van Etten RA, Wahlberg MW, Clayton DA (1980) Cell 22:157–170
Wahleithner JA, Wolstenholme DR (1988) Nucleic Acids Res 16:6897–6913
Walker JE, Saraste M, Runswick MJ, Gay NJ (1982) EMBO J 1:945–951
Walker JE, Fearnley IM, Gay NJ, Gibson BW, Northrop FD, Powell SJ, Runswick MJ, Saraste M, Tybulewicz VLJ (1985) J Mol Biol 184:677–701
Ward BL, Anderson RS, Bendich AJ (1981) Cell 25:793–803
Whisson MB, Spencer MS (1983) Plant Physiol 71:707–711
Young EG, Hanson MR (1987) Cell 50:41–49
Zurawski G, Bottomley W, Whitfeld PR (1982) Proc Natl Acad Sci USA 79:6260–6264
Author information
Authors and Affiliations
Additional information
Communicated by B. B. Sears
Rights and permissions
About this article
Cite this article
Chanut, F.A., Grabau, E.A. & Gesteland, R.F. Complex organization of the soybean mitochondrial genome: recombination repeats and multiple transcripts at the atpA loci. Curr Genet 23, 234–247 (1993). https://doi.org/10.1007/BF00351502
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00351502