Abstract
We have identified a family of small repeated sequences (from 60 to 66 bp in length) in the mitochondrial genome of rice (Oryza sativa cv. Nipponbare). There are at least ten copies of these sequences and they are distributed throughout the mitochondrial genome. Each is potentially capable of forming a stem-and-loop structure and we have designated them PRSs (palindromic repeated sequences). Their features are reminiscent of the small dispersed repeats in the mitochondrial DNA (mtDNA) of some lower eukaryotes, such as Saccharomyces cerevisiae, Neurospora crassa and Chlamydomonas reinhardtii. Some of the PRSs of rice mtDNA are located in the intron of the gene for ribosomal protein S3 (rps3) and in the flanking sequence of the gene for chloroplast-like tRNAAsn (trnN). An analysis of PCR-amplified fragments of these regions from the DNA of some Gramineae suggests that the PRSs were inserted into these regions of the Oryza mtDNA after the divergence of Oryza from the other Gramineae.
Similar content being viewed by others
References
Almasan A, Mishra NC: Recombination by sequence repeats with formation of suppressive or residual mitochondrial DNA in Neurospora. Proc Natl Acad Sci USA 88: 7684–7688 (1991).
André C, Levy A, Walbot V: Small repeated sequences and the structure of plant mitochondrial genomes. Trends Genet 8: 128–132 (1992).
Boer PH, Gray MW: Short dispersed repeats localized in spacer regions of Chlamydomonas reinhardtii mitochondrial DNA. Curr Genet 19: 309–312 (1991).
Coulthart MB, Spencer DF, Gray MW: Comparative analysis of a recombining-repeat-sequence family in the mitochodrial genomes of wheat (Triticum aestivum L.) and rye (Secale cereale L.). Curr Genet 23: 255–264 (1993).
Dale RMK, McClure BA, Houchins JP: A rapid single-stranded cloning strategy for producing a sequential series of overlapping clones for use in DNA sequencing: Application to sequencing the corn mitochodrial 18S rDNA. Plasmid 13: 31–40 (1985).
deZamaroczy M, Bernardi G: The GC clusters of the mitochondrial genome of yeast and their evolutionary origin. Gene 41: 1–22 (1986).
Gualberto JM, Wintz H, Weil J-H, Grienenberger J-M: The genes coding for subunit 3 of NADH dehydrogenase and for ribosomal protein S12 are present in the wheat and maize mitochondrial genomes and are co-transcribed. Mol Gen Genet 215: 118–127 (1988).
Honda H, Hirai A: A simple and efficient method for identification of hybrids using nonradioactive rDNA as probe. Jpn J Breed 40: 339–348 (1990).
Hudspeth MES, Vincent RD, Perlman PS, Shumard DS, Treisman LO, Grossman LI: Expandable var1 gene of yeast mitochondrial DNA: in-frame insertions can explain the strain-specific protein size polymorphisms. Proc Natl Acad Sci USA 81: 3148–3152 (1984).
Hunt MD, Newton KJ: The NCS3 mutation: genetic evidence for the expression of ribosomal protein genes in Zea mays mitochondria. EMBO J 10: 1045–1052 (1991).
Iwahashi M, Nakazono M, Kanno A, Sugino K, Ishibashi T, Hirai A: Genetic and physical maps and a clone bank of mitochondrial DNA from rice. Theor Appl Genet 84: 275–279 (1992).
Joyce PBM, Gray MW: Aspartate and asparagine tRNA genes in wheat mitochondrial DNA: a cautionary note on the isolation of tRNA genes from plants. Nucl Acids Res 17: 7865–7878 (1989).
Lonsdale DM, Hodge TP, Fauron CM-R: The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize. Nucl Acids Res 12: 9249–9261 (1984).
Nakazono M, Hirai A: Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice. Mol Gen Genet 236: 341–346 (1993).
Palmer JD, Shields CR: Tripartite structure of the Brassica campestris mitochondrial genome. Nature 307: 437–440 (1984).
Schon EA, Rizzuto R, Moraes CT, Nakase H, Zeviani M, DiMauro S: A direct repeat is a hotspot for large-scale deletion of human mitochondrial DNA. Science 244: 346–349 (1989)
Sor F, Fukuhara H: Nature of an inserted sequences in the mitochondrial gene coding for the 15S ribosomal RNA of yeast. Nucl Acids Res 10: 1625–1633 (1982)
Weiller G, Schueller CME, Schweyen RJ: Putative target sites for mobile G+C rich clusters in yeast mitochondrial DNA: single elements and tandem arrays. Mol Gen Genet 218: 272–283 (1989).
Weiller GF, Bruckner H, Kim SH, Pratje E, Schweyen RJ: A GC cluster repeat is a hotspot for mit- macro-deletions in yeast mitochondrial DNA. Mol Gen Genet 226: 233–240 (1991).
Yin S, Heckman J, RajBhandary UL: Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria. Cell 26: 325–332 (1981).
Zeviani M, Servidei S, Gellera C, Bertini E, DiMauro S, DiDonato S: An autosomal dominant disorder with multiple deletions of mitochondrial DNA starting at the D-loop region. Nature 339: 309–311 (1989).
Zinn AR, Pohlman JK, Perlman PS, Butow RA: In vivo double-strand breaks occur at recombinogenic G+C-rich sequences in the yeast mitochondrial genome. Proc Natl Acad Sci USA 85: 2686–2690 (1988).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Nakazono, M., Kanno, A., Tsutsumi, N. et al. Palindromic repeated sequences (PRSs) in the mitochondrial genome of rice: evidence for their insertion after divergence of the genus Oryza from the other Gramineae. Plant Mol Biol 24, 273–281 (1994). https://doi.org/10.1007/BF00020167
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00020167