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Phenylalanine ammonia-lyase gene organization and structure


Phenylalanine ammonia-lyase (PAL; EC genomic sequences were isolated from bean (Phaseolus vulgaris L.) genomic libraries using elicitor-induced bean PAL cDNA sequences as a probe. Southern blot hybridization of genomic DNA fragments revealed three divergent classes of PAL genes in the bean genome. Polymorphic forms were observed within each class. The nucleotide sequences of two PAL genes, gPAL2 (class II) and gPAL3 (class III), were determined. gPAL2 contains an open reading frame encoding a polypeptide of 712 amino acids, interrupted by a 1720 bp intron in the codon for amino acid 130. gPAL3 encodes a polypeptide of 710 amino acids showing 72% similarity with that encoded by gPAL2, and contains a 447 bp intron at the same location. At the nucleotide level, gPAL2 and gPAL3 show 59% sequence similarity in exon I, 74% similarity in exon II, and extensive sequence divergence in the intron, 5′ and 3′ flanking regions. S1 nuclease protection identified transcription start sites of gPAL2 and gPAL3 respectively 99 bp and 35 bp upstream from the initiation codon ATG, and showed that gPAL2 but not gPAL3 was activated by elicitor, whereas both were activated by wounding of hypocotyls. The 5′ flanking region of both genes contain TATA and CAAT boxes, and sequences resembling the SV40 enhancer core. gPAL2 contains a 40 bp palindromic sequence and a 22 bp motif that are also found at similar positions relative to the TATA box in 5′ flanking regions of other elicitor-induced bean genes.

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  1. 1.

    Alibert G, Ranjeva R, Boudet A: Recherches sur les enzymes catalysant la formation des acides phénoliques chez Quercus pedunculata (Ehrh.) II. Localisation intracellulaire de la phenylalanine ammoniaque-lyase, de la cinnamate 4-hydroxylase, et de la ‘benzoate synthase’. Biochim Biophys Acta 279: 282–289 (1972).

    PubMed  Google Scholar 

  2. 2.

    Berry-Lowe SL, McKnight TD, Shah DM, Meager RB: The nucleotide sequence, expression, and evolution of one member of a multigene family encoding the small subunit of ribulose 1,5-bisphosphate carboxylase in soybean. J Mol Appl Genet 1: 483–498 (1982).

    PubMed  Google Scholar 

  3. 3.

    Biggin M, Farrell PJ, Barrel BG: Transcription and DNA sequence of the Bam HI L fragment of B95–8 Epstein-Barr virus. EMBO J 3: 1083–1090 (1984).

    PubMed  Google Scholar 

  4. 4.

    Bolwell GP, Bell JN, Cramer CL, Schuch W, Lamb CJ, Dixon RA: L-Phenylalanine ammonia-lyase from Phaseolus vulgaris: Characterization and differential induction of multiple forms from elicitor-treated cell suspension cultures. Eur J Biochem 149: 411–419 (1985).

    PubMed  Google Scholar 

  5. 5.

    Bolwell GP, Sap J, Cramer CL, Lamb CJ, Schuch W, Dixon RA. L-Phenylalanine ammonia-lyase from Phaseolus vulgaris: Partial degradation of enzyme subunits in vitro and in vivo. Biochim Biophys Acta 881: 210–221 (1986).

    Google Scholar 

  6. 6.

    Boudet A, Ranjeva R, Gadal P: Proprietés allostériques spécifiques des deux isoenzymes de la phénylalanine ammoniaque-lyase chez Quercus pedonculata. Phytochemistry 10: 997–1005 (1971).

    Article  Google Scholar 

  7. 7.

    Breathnach U, Chambon P: Organization and expression of eukaryotic split genes coding for proteins. Annu Rev Biochem 50: 349–384 (1981).

    Article  PubMed  Google Scholar 

  8. 8.

    Broglie R, Coruzzi G, Lamppa G, Keith B, Chua N-H: Structural analysis of nuclear genes coding for the precursor to the small subunit of wheat ribulose 1,5-bis-phosphate carboxylase. Biotechnology 1: 55–61 (1983).

    Article  Google Scholar 

  9. 9.

    Chappell J, Hahlbrock K: Transcription of plant defense genes in response to UV light or fungal elicitor. Nature 311: 76–78 (1984).

    Google Scholar 

  10. 10.

    Chomczynski P, Qasba PK: Alkaline transfer of DNA to plastic membranes. Biochem Biophys Res Comm 122: 340–344 (1984).

    PubMed  Google Scholar 

  11. 11.

    Coruzzi G, Broglie R, Edwards C, Chua N-H: Tissue-specific and light-regulated expression of a pea nuclear gene encoding the small subunit of ribulose 1,5-bisphosphate carboxylase. EMBO J 3: 1671–1679 (1984).

    PubMed  Google Scholar 

  12. 12.

    Cramer CL, Bell JN, Ryder TB, Bailey JA, Schuch W, Bolwell GP, Robbins MP, Dixon RA, Lamb CJ: Coordinated synthesis of phytoalexin biosynthetic enzymes in biologically-stressed cells of bean (Phaseolus vulgaris L.). EMBO J 4: 285–289 (1985).

    Google Scholar 

  13. 13.

    Cramer CL, Ryder TB, Bell JN, Lamb CJ: Rapid switching of plant gene expression by fungal elicitor. Science 227: 1240–1243 (1985).

    Google Scholar 

  14. 14.

    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 mitochondrial 18S rDNA. Plasmid 13: 31–40 (1985).

    PubMed  Google Scholar 

  15. 15.

    Dixon RA, Dey PM, Lamb CJ: Phytoalexins: Molecular biology and enzymology. Adv Enzymol Relat Areas Mol Biol 55: 1–135 (1983).

    PubMed  Google Scholar 

  16. 16.

    Dixon RA, Bailey JA, Bell JN, Bolwell GP, Cramer CL, Edwards K, Hamdan MAMS, Lamb CJ, Robbins MP, Ryder TB, Schuch W: Rapid changes in gene expression in response to microbial elicitation. Phil Trans Royal Soc B 314: 411–426 (1986).

    Google Scholar 

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Cramer, C.L., Edwards, K., Dron, M. et al. Phenylalanine ammonia-lyase gene organization and structure. Plant Mol Biol 12, 367–383 (1989).

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Key words

  • elicitor
  • gene family
  • gene sequence
  • Phaseolus vulgaris
  • phenylalanine ammonia-lyase
  • phenylpropanoid biosynthesis