Skip to main content
SpringerLink
Log in

The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana

  • Research Article
  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

Abstract

Phenylpropanoid derivatives are a complex class of secondary metabolites that have many important roles in plants during normal growth and in responses to environmental stress. Phenylalanine ammonialyase (PAL) catalyzes the first step in the biosynthesis of phenylpropanoids, and is usually encoded by a multi-gene family. Genomic clones for three Arabidopsis thaliana PAL genes containing the entire protein-coding region and upstream and downstream sequences have been obtained and completely sequenced. Two A. thaliana PAL genes (PAL1 and PAL2) are structurally similar to PAL genes that have been cloned from other plant species, with a single intron at a conserved position, and a long highly conserved second exon. Previously identified promoter motifs plus several additional sequence motifs were found in the promoter regions of PAL1 and PAL2. Expression of PAL1 and PAL2 is both qualitatively and quantitatively similar in different plant organs and under various inductive conditions. A third A. thaliana PAL gene, PAL3, differs significantly from PAL1 and PAL2 and other sequenced plant PAL genes. PAL3 contains an additional intron, and its deduced amino acid sequence is less homologous to other PAL proteins. The PAL3 promoter region lacks several sequence motifs conserved between A. thaliana PAL1 and PAL2, as well as motifs described in other genes involved in phenylpropanoid metabolism. A. thaliana PAL3 was expressed at very low levels under the conditions examined.

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. Alberts BM, Bray D, Lewis J, Raff M, Roberts K, Watson JD: Molecular Biology of the Cell. Garland Publishing, New York/London (1994).

    Google Scholar 

  2. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current Protocols in Molecular Biology. Greene Publishing Associates/John Wiley, New York (1993).

    Google Scholar 

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

    Google Scholar 

  4. Collinge DB, Slusarenko AJ: Plant gene expression in response to pathogens. Plant Mol Biol 9: 389–410 (1987).

    Google Scholar 

  5. Cramer CL, Bell JN, Ryder TB, Bailey JA, Schuh 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: 285–289 (1985).

  6. Cramer CL, Edwards K, Dron M, Liang X, Dildine SL, Bolwell GP, Dixon RA, Lamb CJ, Schuch WW: Phenylalanine ammonia-lyase gene organization and structure. Plant Mol Biol 12: 367–383 (1989).

    Google Scholar 

  7. daCosta e Silva O, Klein L, Schmelzer E, Trezzini GF, Hahlbrock K: BPF-1, a pathogen-induced DNA-binding protein involved in the plant defense response. Plant J 4: 125–135 (1993).

    Google Scholar 

  8. Davis KR: Arabidopsis thaliana as a model host for studying plant-pathogen interactions. In: Verma DPS (eds) Molecular Signals in Plant-microbe Communications, pp. 393–406, CRC Press, Boca Raton, FL (1992).

    Google Scholar 

  9. Davis KR, Ausubel FM: Characterization of elicitor-induced defense responses in suspension-cultured cells of Arabidopsis. Mol Plant-Microbe Interact 2: 363–368 (1989).

    Google Scholar 

  10. Davis KR, Schott E, Ausubel FM: Virulence of selected phytopathogenic pseudomonads in Arabidopsis thaliana. Mol Plant-Microbe Interact 4: 477–788 (1991).

    Google Scholar 

  11. Davis KR, Schott E, Dong X, Ausubel FM: Arabidopsis thaliana as a model system for studying plant-bacterial interactions. In: Lugtenberg BJJ (eds) Signal Molecules in Plants and Plant-Microbe Interactions, pp. 99–106. Spinger-Verlag, Berlin (1989).

    Google Scholar 

  12. Dellaporta SL, Wood J, Hicks JB: A plant DNA mini-preparation: version 2. Plant Mol Biol Rep 1: 19–22 (1983).

    Google Scholar 

  13. Dong X, Mindrinos M, Davis K, Ausubel F: Induction of Arabidopsis defense genes by virulent and avirulent Pseudomonas syringae strains and by a cloned avirulence gene. Plant Cell 3: 61–72 (1991).

    Google Scholar 

  14. Edwards K, Cramer CL, Bolwell PG, Dixon RA, Schuch W. Lamb CJ: Rapid transient induction of phenylalanine ammonia-lyase mRNA in elicitor-treated bean cells. Proc Natl Acad Sci USA 82: 6731–6735 (1985).

    Google Scholar 

  15. Frank RL, Vodkin LO: Sequence and structure of a phenylalanine ammonia-lyase gene from Glycine max. J DNA Sequencing Mapping 1: 335–346 (1991).

    Google Scholar 

  16. Gowri G, Paiva NL, Dixon RA: Stress responses in alfalfa (Medicago sativa). 12. Sequence analysis of phenylalanine ammonia-lyase (PAL) cDNA clones and appearance of PAL transcripts in elicitor-treated cell cultures and developing plants. Plant Mol Biol 17: 415–429 (1991).

    Google Scholar 

  17. GCG Wisconsin Sequence Analysis Software Package, VMS 6.1 through 7.3, Genetics Computing Group (1991; 1993).

  18. Hahlbrock K, Scheel D: Physiology and molecular biology of phenylpropanoid metabolism. Annu Rev Plant Physiol Plant Mol Biol 40: 347–369 (1989).

    Google Scholar 

  19. Joos HJ, Hahlbrock K: Phenylalanine ammonia-lyase in potato (Solanum tuberosum L.) Genomic complexity, structural comparison of 2 selected genes and modes of expression. Eur J Biochem 204: 621–629 (1992).

    Google Scholar 

  20. Kawamata S, Yamada T, Tanaka Y, Sriprasertsak P, Kato H, Ichinose Y, Kato H, Shiraishi T, Oku H: Molecular cloning of phenylalanine ammonia-lyase cDNA from Pisum sativum. Plant Mol Biol 20: 167–170 (1992).

    Google Scholar 

  21. Kuhn DN, Chappell J, Boudet A, Hahlbrock K: Induction of phenylalanine ammonia-lyase and 4-coumarate: CoA ligase mRNAs in cultured plant cells by UV light or fungal elicitors. Proc Natl Acad Sci USA 81: 1102–1106 (1984).

    Google Scholar 

  22. Lawton MA, Lamb CJ: Transcriptional activation of plant defense genes by fungal elicitor, wounding, and infection. Mol Cell Biol 7: 335–341 (1987).

    Google Scholar 

  23. Lee SW, Robb J, Nazar RN: Truncated phenylalanine ammonia-lyase expression in tomato (Lycopersicon esculentum). J Biol Chem 267: 11824–11830 (1992).

    Google Scholar 

  24. Leyva A, Liang XW, Pintortoro JA, Dixon RA, Lamb CJ: cis-Element combinations determine phenylalanine ammonia-lyase gene tissue-specific expression patterns. Plant Cell 4: 263–271 (1992).

    Google Scholar 

  25. Liang X, Dron M, Cramer CL, Dixon RA, Lamb CJ: Differential regulation of phenylalanine ammonia-lyase genes during plant development and by environmental cues. J Biol Chem 264: 14486–14492 (1989).

    Google Scholar 

  26. Liang X, Dron M, Schmid J, Dixon RA, Lamb CJ: Development and environmental regulation of a phenylalanine ammonia-lyase-β-glucuronidase gene fusion in transgenic tobacco plants. Proc Natl Acad Sci USA 86: 9284–9288 (1989).

    Google Scholar 

  27. Lois R, Dietrich A, Hahlbrock K, Schulz W: A phenylalanine ammonia-lyase gene from parsley: structure, regulation and identification of elicitor and light responsive cis-acting elements. EMBO J 8: 1641–1648 (1989).

    Google Scholar 

  28. Lois R, Hahlbrock K: Differential wound activation of members of the phenylalanine ammonia-lyase and 4-coumarate-CoA ligase gene families in various organs of parsley plants. Z Naturforsch C 47: 90–94 (1992).

    Google Scholar 

  29. Minami E, Ozeki Y, Matsuoka M, Koizuka N, Tanaka Y. Structure and some characterization of the gene for phenylalanine ammonia-lyase from rice plants. Eur J Biochem 185: 19–25 (1989).

    Google Scholar 

  30. Minami E, Tanaka Y: Nucleotide sequence of the gene for phenylalanine ammonia lyase of rice and its deduced amino acid sequence. Biochem Biophys Acta 1171: 321–322 (1993).

    Google Scholar 

  31. Ohl S, Hedrick SA, Chory J, Lamb CJ: Functional properties of a phenylalanine ammonia-lyase promoter from Arabidopsis. Plant Cell 2: 837–848 (1990).

    Google Scholar 

  32. Sharma YK, Davis KR. Ozone-induced expression of stress-related genes in Arabidopsis thaliana. Plant Physiol 105: 1089–1096 (1994).

    Google Scholar 

  33. Shufflebottom D, Edwards K, Schuch W, Bevan M: Transcription of two members of a gene family encoding phenylalanine-lyase leads to remarkably different cell specificities and induction patterns. Plant J 3: 835–845 (1993).

    Google Scholar 

  34. Somssich I, Bollmann J, Hahlbrock K, Kombrink E, Schulz W: Differential early activation of defense-related genes in elicitor-treated parsley cells. Plant Mol Biol 12: 227–234 (1989).

    Google Scholar 

  35. Subramaniam R, Reinold S, Molitor EK, Douglas CJ: Structure, inheritance; and expression of hybrid poplar (Populus trichocarpa × Populus deltoides) phenylalanine ammonia-lyase genes Plant Physiol 102: 71–83 (1993).

    Google Scholar 

  36. Swofford DL: Phylogenetic Analysis Using Parsimony, 3.1.1, Smithsonian Institute (1993).

  37. Tanaka Y, Matsuoka M, Yamanoto N, Ohashi Y, Kano-Murakami Y, Ozeki Y: Structure and characterization of a cDNA clone for phenylalanine ammonia-lyase from cut-injured roots of seet potato. Plant Physiol 90: 1403–1407 (1989).

    Google Scholar 

  38. Wanner LA, Mittal S, Davis KR: Recognition of the avirulence gene avrB from Pseudomonas syringae pv. glycinea by Arabidopsis thaliana. Mol Plant-Microbe Interact 6: 582–591 (1993).

    Google Scholar 

  39. Whetten RW, Phenylalanine ammonia-lyase from loblolly pine: purification of the enzyme and isolation of complementary DNA clones. Plant Physiol 98: 380–386 (1992).

    Google Scholar 

  40. Yamada T, Tanaka Y, Sriprasertsak P, Kato H, Hashimoto T, Kawamata S, Ichinose Y, Kato H, Shiraishi T, Oku H. Phenylalanine ammonia-lyase genes from Pisum sativum: structure, organ-specific expression and regulation by fungal elicitor and suppressor. Plant Cell Physiol 33: 715–725 (1992).

    Google Scholar 

  41. Yu LM, Lamb CJ, Dixon RA: Purification and biochemical characterization of proteins which bind to the H-box cis-element implicated in transcriptional activation of plant defense genes. Plant J 3: 805–816 (1993).

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Ohio State Biotechnology Center, 1060 Carmack Road

    Leslie A. Wanner, Doreen Ware & Keith R. Davis

  2. Department of Plant Biology, The Ohio State University, 43210, Columbus, OH, USA

    Guoqing Li & Keith R. Davis

  3. Abteilung Biochemie, Max-Planck-Institut für Züchtungforschung, Köln, Germany

    Imre E. Somssich

Authors
  1. Leslie A. Wanner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Guoqing Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Doreen Ware
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Imre E. Somssich
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Keith R. Davis
    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

Wanner, L.A., Li, G., Ware, D. et al. The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana . Plant Mol Biol 27, 327–338 (1995). https://doi.org/10.1007/BF00020187

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00020187

Key words

Search

Navigation