Abstract
Most of the plant mitochondrial (mt) genomes that have been mapped are believed to be organized as master circle molecules from which sub-genomic molecules arise through homologous recombination. We have evidence to suggest that a major part of the rice mt genome is organized as independent, sub-genomic molecules or mt chromosomes, one of which has already been mapped. This study is aimed at the identification of the other molecular entities that comprise the genome.
Pulsed-field gel electrophoresis of the native rice mt DNA and Southern analysis with different mt gene probes have shown that in addition to the 117 kb mt chromosome, at least four more such molecules of sizes 130 kb, 95 kb, 70 kb and 56 kb account for most of the rice mt genome. A majority of the rice mt genes that encode products involved in oxidative phosphorylation are distributed among these five chromosomes. Partial restriction map of the 95 kborf 25/cox 3 chromosome, indicating the sites for the enzymesBglII andHindIII has also been determined.
Similar content being viewed by others
References
Bendich A J 1993 Reaching for the ring: the study of mitochondrial genome;Curr. Genet. 24 279–290
Braun C J and Levings III C S 1985 Nucleotide Sequence of the F1-Atpase α-subunit gene from maize mitochondria;Plant Physiol. 79 571–577
Bendich A J, Loretz C J and Monnat R J Jr 1993 The structure of the plant mitochondrial genome; inPlant mitochondria (eds) A Brennicke and U Kuck (VCH Weinheim) pp 171–180
Bendich A J and Smith S B 1990 Moving pictures and pulsedfield gel electrophoresis show linear DNA molecules from chloroplast and mitochondria;Curr. Genet. 17 421–425
Chu G, Vollrath D and Davis R W 1986 Separation of large DNA molecules by contour-clamped homogeneous electric fields;Science 234 1582–1585
Dewey R E, Levings III C S and Timothy D H 1985 Nucleotide sequence of ATPase subunit 6 gene of maize mitochondria;Plant Physiol. 79 914–919
Hiesel R, Schobel W, Schuster W and Brennicke A 1987 The Cytochrome oxidase subunit I and subunitIII genes in Oenothera mitochondria are transcribed from identical promoter sequences;EMBO J. 6 29–34
Houchins J P, Ginsburg H, Rohrbaugh M, Dale R M K, Schardl C L, Hodge T P and Lonsdale D M 1986 DNA sequence analysis of a 5.27 kb direct repeat occurring adjacent to the regions of S-episome homology in maize mitochondria;EMBO J. 5 2781–2788
Iwahashi M, Nakazono M, Kanno A, Sugino K, Ishibashi T and Hirai A 1992 Genetic and physical maps and a clone bank of mitochondrial DNA from rice;Theor. Appl. Genet. 84 275–279
Kadowaki K, Suzuki T, Kazama S, Oh-fuchi T and Sakamoto W 1989 Nucleotide sequence of the cytochrome oxidase sub-unit I gene from rice mitochondria;Nucleic Acids Res. 17 7519
Kaleikau E K, Andre C P, Doshi B and Walbot V 1990a Sequence of the rice mitochondrial gene for apocytochrome b;Nucleic Acids Res. 18 372
Kaleikau E K, Andre C P and Walbot V 1990b Sequence of the FO-ATPase proteolipid (atp 9) gene from rice mitochondria;Nucleic Acids Res. 18 370
Kaleikau E K, Andre C P and Walbot V 1992 Structure and expression of the rice mitochondrial apocytochrome b gene (cob 1) and pseudogene (cob 2);Curr. Genet. 22 463–470
Kao T, Moon E and Wu R 1984 Cytochrome oxidase subunit II gene of rice has an insertion sequence within the intron;Nucleic Acids Res. 12 7305–7315
Levings III C S and Brown G G 1989 Molecular biology of plant mitochondria;Cell 56 171–179
Levy A A, Andre C P and Walbot V 1991 Analysis of a 120-kilobase mitochondrial chromosome in maize;Genetics 128 417–24
Liu A W, Narayanan K K, Andre C P, Kaleikau E K and Walbot V 1992 Co-transcription of orf 25 and cox 3 in rice mitochondria;Curr. Genet. 21 507–513
Lonsdale D M 1984 A review of the structure and organization of the mitochondrial genome of higher plants;Plant Mol. Biol. 3 201–206
Lonsdale D M 1989 The plant mitochondrial genome; inBiochemistry of plants: A comprehensive treatise (eds) P K Stump and E E Lonn (New York: Academic Press) vol. 15, pp 229–295
Lonsdale D M, Hodge T P and Fauron C M-R 1984 The physical map and organization of the mitochondrial genome from the fertile cytoplasm of maize;Nucleic Acids Res. 12 9249–9261
Mulligan R M, Maloney A P and Walbot V 1988 RNA processing and multiple transcription initiation sites results in transcript heterogeneity in maize mitochondria;Mol.Gen. Genet. 211 373–380
Narayanan K K, Andre C P, Yang J and Walbot V 1993 Organization of a 117-kb circular mitochondrial chromosome in IR 36 rice;Curr. Genet. 23 248–254
Newton K J 1988 Plant mitochondrial genome: Organization, expression and variation;Annu. Rev. Plant Physiol. Plant Mol. Biol. 39 503–532
Palmer J D 1988 Intraspecific variation and multicircularity inBrassica mitochondrial DNAs;Genetics 118 341–351
Palmer J D and Shields C R 1984 Tripartite structure of theBrassica compestris mitochondrial genome;Nature (London) 307 437–440
Quetier F, Lejeune B, Delorme S and Falconet D 1985 The molecular organization and expression of the mitochondrial genome of higer plants; inEncyclopedia of plant physiology (eds) R Douce and D A Day (Berlin: Springer Verlag) vol. 18, pp 25–36
Sambrook J, Fritsch E F and Maniatis T 1989Molecular cloning: a laboratory manual 2nd edition (New York: Cold Spring Harbor Laboratory)
Schwartz D A and Cantor C R 1984 Separation of yeast chromosome-sized DNAs by pulsed-field gradient gel electrophoresis;Cell 37 67–75
Small I D, Isaac P G and Leaver C J 1987 Stoichiometric differences in DNA molecules containing the atp A gene suggest mechanisms for the generation of mitochondrial genome diversity in maize;EMBO J. 6 865–869
Wang B, Cheng W, Li Y-N and Li D-D 1989 Some physicochemical properties of rice mitochondrial DNA;Theor. Appl. Genet. 77 581–586
Yamato K, Ogura Y, Kanegal T, Yamada Y and Ohyama K 1992 Mitochondrial genome structure of rice suspension culture from cytoplasmic male-sterile line (A-58 CMS): Reappraisal of the master circle;Theor. Appl. Genet. 83 279–288
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Senthilkumar, P., Narayanan, K.K. Analysis of rice mitochondrial genome organization using pulsed-field gel electrophoresis. J. Biosci. 24, 215–222 (1999). https://doi.org/10.1007/BF02941203
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/BF02941203