Skip to main content
SpringerLink
Log in

Classification and characterization of the rice α-amylase multigene family

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

To establish the size and organization of the rice α-amylase multigene family, we have isolated 30 α-amylase clones from three independent genomic libraries. Partial characterization of these clones indicates that they fall into 5 hybridization groups containing a total of 10 genes. Two clones belonging to the Group 3 hybridization class have more than one gene per cloned fragment. The nucleotide sequence of one clone from Group 1, λOSg2, was determined and compared to other known cereal α-amylase sequences revealing that λOSg2 is the genomic analog of the rice cDNA clone, pOS103. The rice α-amylase genes in Group 1 are analogous to the α-Amy1 genes in barley and wheat. λOSg2 contains sequence motifs common to most actively transcribed genes in plants. Two consensus sequences, TAACA AG A and TATCCAT, were found in the 5′ flanking regions of α-amylase genes of rice, barley and wheat. The former sequence may be specific to α-amylase gene while the latter sequence may be related to a ‘CATC’ box found in many plant genes. Another sequence called the pyrimidine box ( CT CTTTT CT ) was found in the α-amylase genes as well as other genes regulated by gibberellic acid (GA). Comparisons based on amino acid sequence alignment revealed that the multigene families in rice, barley and wheat shared a common ancestor which contained three introns. Some of the descendants of the progenitor α-amylase gene appear to have lost the middle intron while others maintain all three introns.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Akazawa T, Hara-Nishimura I: Topographic aspects of biosynthesis, extracellular secretion, and intracellular storage of proteins in plant cells. Ann Rev Plant Physiol 36: 441–472 (1985).

    Google Scholar 

  2. Baulcombe DC, Barker RF, Jarvis MG: A gibberellin responsive wheat gene has homology to yeast carboxypeptidase Y. J Biol Chem 262: 13726–13735 (1987).

    PubMed  Google Scholar 

  3. Baulcombe DC, Huttly AK, Martienssen RA, Barker RF, Jarvis MG: A novel wheat α-amylase gene (α-Amy3). Mol Gen Genet 209: 33–40 (1987).

    Article  Google Scholar 

  4. Beltz GA, Jacobs KA, Eickbush TH, Cherbas PT, Kafatos FC: Isolation of multigene families and determination of homologies by filter hybridization methods. Meth Enzymol 100: 266–285 (1983).

    PubMed  Google Scholar 

  5. Benfey PN, Chua NH: Regulated genes in transgenic plants. Science 244: 174–181 (1989).

    Google Scholar 

  6. Biggin MD, Gibson TJ, Hong GF: Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci USA 80: 3963–3965 (1983).

    PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  8. Chandler PM, Zwar JA, Jacobsen JV, Higgins TJV, Inglis AS: The effects of gibberellic acid and abscisic acid on α-amylase mRNA levels in barley aleurone layers studies using an α-amylase cDNA clone. Plant Mol Biol 3: 407–418 (1984).

    Google Scholar 

  9. Daussant J, Miyata S, Mitsui T, Akazawa T: Enzymic mechanism of starch breakdown in germinating rice seeds, 15. Immunological study on multiple forms of amylase. Plant Physiol 71: 88–95 (1983).

    Google Scholar 

  10. Deikman J, Jones RL: Control of α-amylase mRNA accumulation by gibberellic acid and calcium in barley aleurone layers. Plant Physiol 78: 192–198 (1985).

    Google Scholar 

  11. Devereux J, Haeberli P, Smithies O: A comprehensive set of sequence analysis programs for the VAX. Nucl Acids Res 12: 387–395 (1984).

    PubMed  Google Scholar 

  12. Doolittle WF: The Origin and function of intervening sequences in DNA: A review. Am Nat 130: 915–928 (1987).

    Article  Google Scholar 

  13. Feinberg AP, Vogelstein B: A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6–13 (1983).

    PubMed  Google Scholar 

  14. Feinberg AP, Vogelstein B: A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity: addendum. Anal Biochem 137: 266–267 (1984).

    PubMed  Google Scholar 

  15. Fischer RL, Goldberg RB: Structure and flanking regions of soybean seed protein genes. Cell 29: 651–660 (1982).

    Article  PubMed  Google Scholar 

  16. Forde BG, Heyworth A, Pywell J, Kreis M: Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize. Nucl Acids Res 13: 7327–7339 (1985).

    PubMed  Google Scholar 

  17. Gale MD, Law CN, Chojecki AJ, Kempton RA: Genetic control of α-amylase production in wheat. Theor Appl Genet 64: 309–316 (1983).

    Article  Google Scholar 

  18. Gluzman Y, Shenk T (eds): Enhancers and Eukaryotic Gene Expression: Current Communications in Molecular Biology. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1983).

    Google Scholar 

  19. Hanley BA, Schuler MA: Plant intron sequences: evidence for distinct groups of introns. Nucl Acids Res 16: 7159–7176 (1988).

    PubMed  Google Scholar 

  20. Henikoff S: Unidirectional digestion with exonuclease III in DNA sequence analysis. Meth Enzymol 155: 156–165 (1988).

    Google Scholar 

  21. Huttly AK, Baulcombe DC: A wheat α-Amy2 promoter is regulated by gibberellin in transformed oat aleurone protoplasts. EMBO J 8: 1907–1913 (1989).

    Google Scholar 

  22. Huttly AK, Martienssen RA, Baulcombe DC: Sequence heterogeneity and differential expression of the α-Amy2 gene family in wheat. Mol Gen Genet 214: 232–240 (1988).

    PubMed  Google Scholar 

  23. Jacobsen JV, Higgins TJV: Characterization of the α-amylase synthesized by aleurone layers of himalaya barley in response to gibberellic acid. Plant Physiol 70: 1647–1653 (1982).

    Google Scholar 

  24. Jones RL, Carbonell J: Regulation of the synthesis of barley aleurone α-amylase by gibberellic acid and calcium ions. Plant Physiol 76: 213–218 (1984).

    Google Scholar 

  25. Joshi CP: An inspection of domain between putative TATA box and translation start site in 79 plant genes. Nucl Acids Res 15: 6643–6653 (1987).

    PubMed  Google Scholar 

  26. Joshi CP: Putative polyadenylation signals in nuclear genes of higher plants: a compilation and analysis. Nucl Acids Res 15: 9627–9640 (1987).

    PubMed  Google Scholar 

  27. Khursheed B, Rogers JC: Barley α-amylase genes. J Biol Chem 263: 18953–18960 (1988).

    PubMed  Google Scholar 

  28. Knox CAP, Sonthayanon B, Chandra GR, Muthukrishnan S: Structure and organization of two divergent α-amylase genes from barley. Plant Mol Biol 9: 3–17 (1987).

    Google Scholar 

  29. Maier UG, Brown JWS, Toloczyki C, Feix G: Binding of a nuclear factor to a consensus sequence in the 5′ flanking region of zein genes from maize. EMBO J 6: 17–22 (1987).

    Google Scholar 

  30. Maniatis T, Fritsch EF, Sambrook J: Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory. Cold Spring Harbor, NY (1982).

    Google Scholar 

  31. Mitchell PJ, Tjian R: Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 245: 371–378 (1989).

    PubMed  Google Scholar 

  32. Mitsui T, Christeller JT, Hara-Nishimura I, Akazawa T: Possible roles of calcium and calmodulin in the biosynthesis and secretion of α-amylase in rice seed scutellar epithelium. Plant Physiol 75: 21–25 (1984).

    Google Scholar 

  33. Miyata S, Akazawa T: Enzymic Mechanism of starch breakdown in germinating rice seeds 12. Biosynthesis of α-amylase in relation to protein glycosylation. Plant Physiol 70: 147–153 (1982).

    Google Scholar 

  34. Mizusawa S, Nishimura S, Seela F: Improvement of dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP. Nucl Acids Res 14: 1319–1324 (1986).

    PubMed  Google Scholar 

  35. Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8: 4321–4325 (1980).

    PubMed  Google Scholar 

  36. Nagy F, Fluhr R, Kuhlemeier C, Kay S, Boutry M, Green P, Poulsen C, Chua NH: Cis-acting elements for selective expression of two photosynthetic genes in transgenic plants. Phil Trans R Soc Lond B 314: 493–500 (1986).

    Google Scholar 

  37. Nei M: Molecular Evolutionary Genetics. Columbia University Press, New York (1987).

    Google Scholar 

  38. O'Neill SD, Kumagai M, Majumdar A, Huang N, Sutliff TD, Rodriguez RL: The α-amylase genes in Oryza sativa: Characterization of cDNA clones and mRNA expression during seed germination. Mol Gen Genet (in press).

  39. Ou-Lee T, Turgeon R, Wu R: Interaction of a gibberellin-induced factor with the upstream region of an α-amylase gene in rice aleurone tissue. Proc Natl Acad Sci USA 85: 6366–6369 (1988).

    PubMed  Google Scholar 

  40. Rahmatullah RJ, Huang JK, Clark KL, Reeck GR, Chandra GR and Muthukrishnan S: Nucleotide and predicted amino acid sequences of two different genes for high-pI α-amylase from barley. Plant Mol Biol 12: 119–121 (1989).

    Google Scholar 

  41. Rogers JC, Milliman C: Coordinate increase in major transcripts from the high pI α-amylase multigene family in barley aleurone cells stimulated with gibberellic acid. J Biol Chem 259: 12234–12240 (1984).

    PubMed  Google Scholar 

  42. Rogers JC, Milliman C: Isolation and sequence analysis of a barley α-amylase cDNA clone. J Biol Chem 258: 8169–8174 (1983).

    PubMed  Google Scholar 

  43. Rogers JC: Two barley α-amylase gene families are regulated differently in aleurone cells. J Biol Chem 260: 3731–3738 (1985).

    Google Scholar 

  44. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW: Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81: 8014–8018 (1984).

    PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  46. Schoffl F, Baumann G, Raschke E, Bevan M: The expression of heat-shock genes in higher plants. Phil Trans R Soc Lond B 314: 453–468 (1986).

    Google Scholar 

  47. Whittier RF, Dean DA, Rogers JC: Nucleotide sequence analysis of α-amylase and thiol protease genes that are hormonally regulated in barley aleurone cells. Nucl Acids Res 15: 2515–2535 (1987).

    PubMed  Google Scholar 

  48. Yamamoto KR, Alberts BM, Benzinger R, Lawhorne L, Treiber G: Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification. Virology 40: 734–744 (1970).

    PubMed  Google Scholar 

  49. Yanisch-Perron C, Vieira J, Messing J: Improved M13 phage cloning vectors and host strains: nucleotides sequences of the M13mp18 and pUC19 vectors. Gene 33: 103–119 (1985).

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. The Department of Genetics, University of California, 95616, Davis, CA, USA

    Ning Huang, Thomas D. Sutliff, James C. Litts & Raymond L. Rodriguez

Authors
  1. Ning Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thomas D. Sutliff
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James C. Litts
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Raymond L. Rodriguez
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Huang, N., Sutliff, T.D., Litts, J.C. et al. Classification and characterization of the rice α-amylase multigene family. Plant Mol Biol 14, 655–668 (1990). https://doi.org/10.1007/BF00016499

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00016499

Key words

Search

Navigation