Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa

Planta

Volumn 238, Issue 3, 2013, Pages 487-497

  Shi, Rui ^a   Shuford, Christopher M ^a   Wang, Jack P ^a   Sun, Ying Hsuan ^a,b   Yang, Zhichang ^a   Chen, Hsi Chuan ^a   Tunlaya Anukit, Sermsawat ^a   Li, Quanzi ^a,c   Liu, Jie ^a   Muddiman, David C ^a   Sederoff, Ronald R ^a   Chiang, Vincent L ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^c SHANDONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Enzyme property; PC IDMS; Phenylalanine ammonia lyase; Populus trichocarpa; Post transcriptional regulation; Protein mRNA ratio; Subcellular localization; Wood formation

Indexed keywords

POPULUS TRICHOCARPA; SUBGROUP A; SUBGROUP B;

PHENYLALANINE AMMONIA LYASE;

ARTICLE; ENZYMOLOGY; GENE EXPRESSION REGULATION; MASS SPECTROMETRY; METABOLISM; PHYSIOLOGY; POPULUS;

GENE EXPRESSION REGULATION, PLANT; MASS SPECTROMETRY; PHENYLALANINE AMMONIA-LYASE; POPULUS;

EID: 84882877816     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-013-1905-1     Document Type: Article

References (48)

1. Achnine L, Blancaflor EB, Rasmussen S, Dixon RA (2004) Colocalization of l-phenylalanine ammonia-lyase and cinnamate 4-hydroxylase for metabolic channeling in phenylpropanoid biosynthesis. Plant Cell 16: 3098-3109.
2. Ahmed H (2005) Principles and reactions of protein extraction. CRC Press, Boca Raton.
3. Appert C, Logemann E, Hahlbrock K, Schmid J, Amrhein N (1994) Structural and catalytic properties of the four phenylalanine ammonia-lyase isoenzymes from parsley (Petroselinum crispum Nym.). Eur J Biochem 225: 491-499.
4. Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LO (2012) Before It gets started: regulating translation at the 5′UTR. Comp Funct Genomics 2012: 475731.
5. Bagal UR, Leebens-Mack JH, Lorenz WW, Dean JF (2012) The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage. BMC Genomics 13(Suppl 3): S1.
6. Bassard JE, Mutterer J, Duval F, Werck-Reichhart D (2012) A novel method for monitoring the localization of cytochromes P450 and other endoplasmic reticulum membrane associated proteins: a tool for investigating the formation of metabolons. FEBS J 279: 1576-1583.
7. Chen HC, Li Q, Shuford C, Liu J, Muddiman D, Sederoff R, Chiang VL (2011) Membrane protein complexes catalyze both 4- and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis. PNAS 108: 21253-21258.
8. Chiang VL (2002) From rags to riches. Nat Biotechnol 20: 557-558.
9. Cochrane FC, Davin LB, Lewis NG (2004) The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry 65: 1557-1564.
10. Czichi U, Kindl H (1975) Formation of p-coumaric acid and o-coumaric acid from l-phenylalanine by microsomal membrane fractions from potato: evidence of membrane-bound enzyme complexes. Planta 125: 115-125.
11. Gao L, Fang Z, Zhang K, Zhi D, Cui X (2011) Length bias correction for RNA-seq. data in gene set analyses. Bioinformatics 27: 662-669.
12. Hrazdina G, Wagner G (1985) Metabolic pathways as enzyme complexes: evidence for the synthesis of phenylpropanoids and flavonoids on membrane-associated enzyme complexes. Arch Biochem Biophys 237: 88-100.
13. Jorrin J, Dixon R (1990) Stress responses in alfalfa (Medicago sativa L.) II. Purification, characterization, and induction of phenylalanine ammonia-lyase Isoforms from elicitor-treated cell suspension cultures. Plant Physiol 92: 447-455.
14. Kao YY, Harding SA, Tsai CJ (2002) Differential expression of two distinct phenylalanine ammonia-lyase genes in condensed tannin-accumulating and lignifying cells of quaking aspen. Plant Physiol 130: 796-807.
15. Lepelley M, Mahesh V, McCarthy J, Rigoreau M, Crouzillat D, Chabrillange N, de Kochko A, Campa C (2012) Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae). Planta 236: 313-326.
16. Li Q, Lin Y, Sun YH, Song J, Chen H, Zhang X, Sederoff R, Chiang VL (2012) Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa. PNAS 109: 14699-14704.
17. Liang XW, Dron M, Cramer CL, Dixon RA, Lamb CJ (1989) Differential regulation of phenylalanine ammonia-lyase genes during plant development and by environmental cues. J Biol Chem 264: 14486-14492.
18. Liu H, Sadygov RG, Yates JR 3rd (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193-4201.
19. Liu J, Shi R, Li Q, Sederoff R, Chiang VL (2012) A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities. Planta 236: 879-885.
20. MacDonald MJ, D'Cunha GB (2007) A modern view of phenylalanine ammonia lyase. Biochem Cell Biol 85: 273-282.
21. Maier T, Schmidt A, Güell M, Kühner S, Gavin AC, Aebersold R, Serrano L (2011) Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 7: 511.
22. Malys N, McCarthy JE (2011) Translation initiation: variations in the mechanism can be anticipated. Cell Mol Life Sci 68: 991-1003.
23. Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNASeq. Nat Methods 5: 621-628.
24. Mosley AL, Sardiu ME, Pattenden SG, Workman JL, Florens L, Washburn MP (2011) Highly reproducible label free quantitative proteomic analysis of RNA polymerase complexes. Mol Cell Proteomics 10: M110. 000687. doi: 10. 1074/mcp. M110. 000687.
25. Motameny S, Wolters S, Nurnberg R, Schumacher B (2010) Next generation sequencing of miRNAs-strategies, resources and methods. Genes 1: 70-84.
26. Nie L, Wu G, Zhang W (2006) Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify of variations. Biochem Biophys Res Commun 339: 603-610.
27. Olsen KM, Lea US, Slimestad R, Verheul M, Lillo C (2008) Differential expression of four Arabidopsis PAL genes; PAL1 and PAL2 have functional specialization in abiotic environmental-triggered flavonoid synthesis. J Plant Physiol 165: 1491-1499.
28. Pietarinen S, Willför S, Vikström F, Holmbom B (2006) Aspen knots, a rich source of flavonoids. J Wood Chem Technol 26: 245-258.
29. Rasmussen S, Dixon RA (1999) Transgene-mediated and elicitor-induced perturbation of metabolic channeling at the entry point into the phenylpropanoid pathway. Plant Cell 11: 1537-1551.
30. Reichert AI, He XZ, Dixon RA (2009) Phenylalanine ammonia-lyase (PAL) from tobacco (Nicotiana tabacum): characterization of the four tobacco PAL genes and active heterotetrameric enzymes. Biochem J 424: 233-242.
31. Rohde A, Morreel K, Ralph J et al (2004) Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism. Plant Cell 16: 2749-2771.
32. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York.
33. Sato T, Takabe K, Fujita M (2004) Immunolocalization of phenylalanine ammonia-lyase and cinnamate-4-hydroxylase in differentiating xylem of poplar. C R Biol 327: 827-836.
34. Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res 39: D670-D676.
35. Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011) Global quantification of mammalian gene expression control. Nature 473: 337-342.
36. Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2013) Corrigendum: global quantification of mammalian gene expression control. Nature 495: 126-127.
37. Shi R, Sun YH, Li Q, Heber S, Sederoff R, Chiang VL (2010a) Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. Plant Cell Physiol 51: 144-163.
38. Shi R, Yang C, Lu S, Sederoff R, Chiang VL (2010b) Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa. Planta 6: 1281-1288.
39. Shuford C, Li Q, Sun YH, Chen H, Wang J, Shi R, Sederoff R, Chiang V, Muddiman D (2012a) Comprehensive quantification of monolignol-pathway enzymes in populus trichocarpa by protein cleavage isotope dilution mass spectrometry. J Proteome Res 11: 3390-3404.
40. Shuford C, Sederoff R, Chiang V, Muddiman D (2012b) Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS). Mol Cell Proteomics 11: 814-823.
41. Studer M, DeMartini J, Davis M, Sykes R, Davison B, Keller M, Tuskan G, Wyman C (2011) Lignin content in natural Populus variants affects sugar release. Proc Natl Acad Sci USA 108: 6300-6305.
42. Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC et al (2004) Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol Cell Proteomics 3: 960-969.
43. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
44. Vermerris W, Nicholson R (2006) Phenolic compound biochemistry. Springer, Berlin, pp 107-108.
45. Vogel C, Marcotte EM (2012) Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet 13: 227-232.
46. Vogt T (2010) Phenylpropanoid biosynthesis. Mol plant 3: 2-20.
47. Wang J, Shuford C, Li Q, Song J, Lin Y, Sun Y, Chen H, Williams C, Muddiman D, Sederoff R, Chiang VL (2012) Functional rRedundancy of the tTwo 5-Hydroxylases in monolignol biosynthesis of populus trichocarpa: lC-MS/MS based protein quantification and metabolic flux analysis. Planta 236: 795-808.
48. Zhang Y, Wen Z, Washburn MP, Florens L (2010) Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem 82: 2272-2281.