Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

Molecular analysis of the gene encoding a rice starch branching enzyme

  • 859 Accesses

  • 53 Citations


The sequence of a rice gene encoding a starch branching enzyme (sbe1) shows extreme divergence from that of the rice gene, that is homologous to bacterial glycogen branching enzyme (sbe2). sbe1 is expressed abundantly and specifically in developing seeds and maximally in the middle stages of seed development. This expression pattern completely coincides with that of the waxy gene, which encodes a granule-bound starch synthase. Three G-box motifs and consensus promoter sequences are present in the 5′ flanking region of sbe1. It encodes a putative transit peptide, which is required for transport into the amyloplast. A 2.2 kb intron (intron 2) precedes the border between the regions encoding the transit peptide and the mature protein, and contains a high G/C content with several repeated sequences in its 5′ half. Although only a single copy of sbe1 is present in the rice genome, Southern analysis using intron 2 as a probe indicates the presence of several homologous sequences in the rice genome, suggesting that this large intron and also the transit peptide coding region may be acquired from another portion of the genome by duplication and insertion of the sequence into the gene.

This is a preview of subscription content, log in to check access.


  1. Anderson JM, Larsen R, Laudencia D, Kim WT, Morrow D, Okita TW, Preiss J (1991) Molecular characterization of the gene encoding a rice endosperm-specific ADP-glucose pyrophosphorylase subunit and its developmental pattern of transcription. Gene 97:199–205

  2. Asaoka M, Okuno K, Sugimoto Y, Fuwa H (1985) Developmental changes in the structure of endosperm starch of rice (Oryza sativa L.). Agri Biol Chem 49:1973–1978

  3. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman TG, Smith TA, Struhl K (1987) Current protocols in molecular biology. Wiley, New York

  4. Baba T, Kimura K, Mizuno K, Etch H, Ishida Y, Shida O, Arai Y (1991) Sequence conservation of the catalytic regions of amylolytic enzymes in maize branching enzyme-I. Biochem Biophys Res Commun 181:87–94

  5. Baecker PA, Greenberg E, Preiss J (1986) Biosynthesis of bacterial glycogen. Primary structure of Escherichia coli 1,4-α-d-glucan 6-α-d-glucano)-transferase as deduced from the nucleotide sequence of the glgB gene. J Biol Chem 261:8738–8743

  6. Benton WD, Davis RW (1977) Screening λgt recombinant clones by hybridization to single plaques in situ. Science 196:180–182

  7. Boyer CD, Preiss J (1978) Multiple forms of (1,4)-α-d-glucan, (1,4)-α-d-glucan-6-glycosyl transferase from developing Zea mays L. kernels. Carbohydr Res 61:321–334

  8. Bhattacharyya MK, Smith AM, Ellis THN, Hedley C, Martin C (1990) The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60:115–122

  9. Breathnach R, Chambon P (1981) Organization and expression of eukaryotic split genes coding for proteins. Annu Rev Biochem 50:349–383

  10. Dang PL, Boyer CD (1988) Maize leaf and kernel starch synthases and starch branching enzyme. Phytochemistry 27:1255–1259

  11. Domon C, Evrard J-L, Pillay DTN, Steinmetz A (1991) A 2.6 kb intron separates the signal peptide coding sequence of an anther-specific protein from the rest of the gene in sunflower. Mol Gen Genet 229:238–244

  12. Gantt JS, Baldauf SL, Colio PJ, Wooden NF, Palmer JD (1991) Transfer of rpl22 to the nucleus greatly preceded its loss from chloroplast and involved the gain of an intron. EMBO J 10:3073–3078

  13. Giuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, Cashmore AR (1988) An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene. Proc Natl Acad Sci USA 85:7089–7093

  14. Goodall GJ, Filipowicz W (1991) Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants. EMBO J 10:2635–2644

  15. Hirano H, Sano Y (1991) Molecular characterization of the waxy locus of rice (Oryza sativa). Plant Cell Physiol 32:989–997

  16. Innis MA, Gelfand DH (1990) Optimization of PCRs. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols a guide to methods and applications. Academic Press, San Diego, Calif., pp 3–12

  17. Kiel JAKW, Boels JM, Beldman G, Venema G (1990) Nucleotide sequence of the Synechococcus sp. PCC7942 branching enzyme gene (glgB): expression in Bacillus subtilis. Gene 89:77–84

  18. Klösgen RB, Gierl A, Schwarz-Sommer Z, Seadler H (1986) Molecular analysis of the waxy locus of Zea mays. Mol Gen Genet 203:237–244

  19. Koßmann J, Visser RGF, Müiller-Röber B, Willmitzer L, Sonnewald U (1991) Cloning and expression analysis of a potato cDNA that encodes branching enzyme: evidence for co-expression of starch biosynthetic genes. Mol Gen Genet 230:39–44

  20. Mizuno K, Kimura K, Arai Y, Kawasaki T, Shimada H, Baba T (1992) Starch branching enzymes from immature rice seeds. J Biochem 112:643–651

  21. Nugent JM, Palmer JD (1991) RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell 66:473–481

  22. Rhode W, Becker D, Salamini F (1988) Structural analysis of the waxy locus from Hordeum vulgare. Nucleic Acids Res 16:7185–7186

  23. Rogers SO, Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol Biol 5:69–76

  24. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467

  25. Smith AM (1988) Major differences in isoforms of starch-branching enzyme between developing embryos of round- and wrinkled-seeded peas (Pisum sativum L.). Planta 175:270–279

  26. Smith AM, Neuhaus HE, Stitt M (1990) The impact of decreased activity of starch-branching enzyme on photosynthetic starch synthesis in leaves of wrinkled-seeded peas. Planta 181:310–315

  27. Wang Z-y, Wu Z-1, Xing Y-y, Zheng F-g, Guo X-1, Zhang W-g, Hong M-m (1990) Nucleotide sequence of rice waxy gene. Nucleic Acids Res 18:5898

Download references

Author information

Correspondence to Hiroaki Shimada.

Additional information

Communicated by R.G. Herrmann

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kawasaki, T., Mizuno, K., Baba, T. et al. Molecular analysis of the gene encoding a rice starch branching enzyme. Molec. Gen. Genet. 237, 10–16 (1993).

Download citation

Key words

  • Gene expression
  • Nucleotide sequence
  • Starch branching enzyme
  • Rice seed development
  • Promoter