Dixon RA, Paiva NL: Stress-induced phenylpropanoid metabolism. Plant Cell. 1995, 7: 1085-1097. 10.1105/tpc.7.7.1085.
Article
PubMed
CAS
PubMed Central
Google Scholar
Pellegrini L, Rohfritsch O, Fritig B, Legrand M: Phenylalanine ammonia-lyase in tobacco: molecular cloning and gene expression during the hypersensitive reaction to tobacco mosaic virus and the response to a fungal elicitor. Plant Physiol. 1994, 106: 877-886. 10.1104/pp.106.3.877.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hamberger B, Ellis M, Friedmann M, de Azevedo SC, Barbazuk B, Douglas CJ: Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene families. Can J Bot. 2007, 85 (12): 1182-1201. 10.1139/B07-098.
Article
CAS
Google Scholar
Naoumkina MA, Zhao Q, Gallego-Giraldo L, Dai X, Zhao PX, Dixon RA: Genome-wide analysis of phenylpropanoid defence pathways. Mol Plant Pathol. 2010, 11 (6): 829-846.
PubMed
CAS
Google Scholar
Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W: Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 2003, 133 (3): 1051-1071. 10.1104/pp.103.026484.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tsai CJ, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y: Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus. New Phytol. 2006, 172 (1): 47-62. 10.1111/j.1469-8137.2006.01798.x.
Article
PubMed
CAS
Google Scholar
MacDonald MJ, D’Cunha GB: A modern view of phenylalanine ammonia lyase. Biochem Cell Biol. 2007, 85: 273-282. 10.1139/O07-018.
Article
PubMed
CAS
Google Scholar
Kim W, Erlandsen H, Surendran S, Stevens RC, Gamez A, Michols-Matalon K, Tyring SK, Matalon R: Trends in enzyme therapy forphenylketonuria. Mol Ther. 2004, 10: 220-224. 10.1016/j.ymthe.2004.05.001.
Article
PubMed
Google Scholar
Kyndt JA, Meyer TE, Cusanovich MA, Van Beeumen JJ: Characterization of a bacterial tyrosine ammonia lyase, a biosynthetic enzyme for the photoactive yellow protein. FEBS Lett. 2002, 512: 240-244. 10.1016/S0014-5793(02)02272-X.
Article
PubMed
CAS
Google Scholar
Moffitt MC, Louie GV, Bowman ME, Pence J, Noel JP, Moore BS: Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization. Biochemistry. 2007, 46: 1004-1012. 10.1021/bi061774g.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ogata K, Uchiyama K, Yamada H: Metabolism of aromatic amino acid in microorganisms. Part I: formation of cinnamic acid from phenylalanine. Agric Biol Chem. 1967, 31: 200-206. 10.1271/bbb1961.31.200.
Article
CAS
Google Scholar
Xiang L, Moore BS: Biochemical characterization of a prokaryotic phenylalanine ammonia lyase. J Bacteriol. 2005, 187: 4286-4289. 10.1128/JB.187.12.4286-4289.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xu F, Cai R, Cheng S, Du H, Wang Y, Cheng S: Molecular cloning, characterization and expression of phenylalanine ammonia-lyase gene from Ginkgo biloba. Afr J Biotechnol. 2008, 7: 721-729.
Google Scholar
Okada T, Mikage M, Sekita S: Molecular characterization of the phenylalanine Ammonia-Lyase from Ephedra sinica. Biol Pharm Bull. 2008, 31: 2194-2199. 10.1248/bpb.31.2194.
Article
PubMed
CAS
Google Scholar
Minami E, Ozeki Y, Matsuoka M, Koizuka N, Tanaka Y: Structure and some characterization of the gene for phenylalanine ammonialyase from rice plants. Eur J Biochem. 1989, 185: 19-25. 10.1111/j.1432-1033.1989.tb15075.x.
Article
PubMed
CAS
Google Scholar
Lu BB, Du Z, Ding RX, Zhang L, Yu XJ, Liu CH, Chen WS: Cloning and characterization of a differentially expressed phenylalanine ammonia-lyase gene (IiPAL) after genome duplication from tetraploid Isatis indigotica Fort. J Integr Plant Biol. 2006, 48 (12): 1439-1449. 10.1111/j.1744-7909.2006.00363.x.
Article
CAS
Google Scholar
Wanner LA, Li G, Ware D, Somssich IE, Davis KR: The phenylalanine ammonia lyase gene family in Arabidopsis thaliana. Plant Mol Biol. 1995, 27: 327-338. 10.1007/BF00020187.
Article
PubMed
CAS
Google Scholar
Gao JH, Zhang SW, Cai F, Zheng XJ, Lin N, Qin XB, Ou YC, Gu XP, Zhu XH, Xu Y, Chen F: Characterization, and expression profile of a phenylalanine ammonia lyase gene from Jatropha curcas L. Mol Biol Rep. 2012, 39: 3443-3452. 10.1007/s11033-011-1116-4.
Article
PubMed
Google Scholar
Jiang YM, Xia N, Li XD, Shen WB, Liang LJ, Wang CY, Wang R, Peng F, Xia B: Molecular cloning and characterization of a phenylalanine ammonia-lyase gene (LrPAL) from Lycoris radiate. Mol Biol Rep. 2011, 38: 1935-1940. 10.1007/s11033-010-0314-9.
Article
PubMed
CAS
Google Scholar
Ritter H, Schulz GE: Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell. 2004, 16: 3426-3436. 10.1105/tpc.104.025288.
Article
PubMed
CAS
PubMed Central
Google Scholar
Joos HJ, Hahlbrock K: Phenylalanine ammonia-lyase in potato (Solanum tuberosumL.). Genomic complexity, structural comparison of two selected genes and modes of expression. Eur J Biochem. 1992, 204: 621-629. 10.1111/j.1432-1033.1992.tb16675.x.
Article
PubMed
CAS
Google Scholar
Chang A, Lim MH, Lee SW, Robb EJ, Nazar RN: Tomato phenylalanine ammonia-lyase gene family, highly redundant but strongly underutilized. J Biol Chem. 2008, 283: 33591-33601. 10.1074/jbc.M804428200.
Article
PubMed
CAS
PubMed Central
Google Scholar
Huang JL, Gu M, Lai ZB, Fan BF, Shi K, Zhou YH, Yu JQ, Chen ZX: Functional analysis of the arabidopsis PAL Gene family in plant growth, development, and response to environmental stress. Plant Physiol. 2010, 153: 1526-1538. 10.1104/pp.110.157370.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schwede TF, Re’tey J, Schulz GE: Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry. 1999, 38: 5355-5361. 10.1021/bi982929q.
Article
PubMed
CAS
Google Scholar
Watanabe SK, Hernandez-Velazco G, Iturbe-Chinas F, Lopez-Munguia A: Phenylalanine ammonia lyase from Sporidiobolus pararoseus and Rhodosporidium toruloides: application for phenylalanine and tyrosine deamination. World J Microbiol Biotechnol. 1992, 8: 406-410. 10.1007/BF01198755.
Article
CAS
Google Scholar
Mukherjee PK, Mukherjee D, Maji AK, Rai S, Heinrich M: The sacred lotus (Nelumbo nucifera)-phytochemical and therapeutic profile. J Pharm Pharmacol. 2009, 61 (4): 407-422.
PubMed
CAS
Google Scholar
Kashiwada Y, Aoshima A, Ikeshiro Y, Chen YP, Furukawa H, Itoigawa M, Fujioka T, Mihashi K, Cosentino LM, Morris-Natschke SL, Lee KH: Anti-HIV benzylisoquinoline alkaloids and flavonoids from the leaves of Nelumbo nucifera, and structure-activity correlations with related alkaloids. Bioorg Med Chem. 2005, 13: 443-448. 10.1016/j.bmc.2004.10.020.
Article
PubMed
CAS
Google Scholar
Hsu J: Late cretaceous and cenozoic vegetation in China, emphasizing their connections with north America. Ann Mo Bot Gard. 1983, 70: 490-508. 10.2307/2992084.
Article
Google Scholar
Ming R, Vanburen R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, et al: Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 2013, 14: R41-10.1186/gb-2013-14-5-r41.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Fan G, Liu Y, Sun F, Shi C, Liu X, Peng J, Chen W, Huang X, Cheng S, Liu Y, Liang X, Zhu H, Bian C, Zhong L, Lv T, Dong H, Liu W, Zhong X, Chen J, Quan Z, Wang Z, Tan B, Lin C, Mu F, Xu X, Ding Y, Guo AY, Wang J, Ke W: The sacred lotus genome provides insights into the evolution of flowering plants. Plant J. 2013, 76: 557-567. 10.1111/tpj.12313.
Article
PubMed
CAS
Google Scholar
Schmidt K, Heberle B, Kurrasch J, Nehls R, Stahl DJ: Suppression of phenylalanine ammonia lyase expression in sugar beet by the fungal pathogen Cercospora beticola is mediated at the core promoter of the gene. Plant Mol Biol. 2004, 55: 835-852. 10.1007/s11103-005-2141-2.
Article
PubMed
CAS
Google Scholar
Angiosperm Phylogeny Group: An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc. 2003, 141: 399-436.
Article
Google Scholar
Rösler J, Krefel F, Amrhein N, Sohmid J: Maize phenylalanine ammonia-lyase activity. Plant Physiol. 1997, 113: 175-179. 10.1104/pp.113.1.175.
Article
PubMed
PubMed Central
Google Scholar
Bagal UR, Leebens-Mack JH, Lorenz WW, Dean JFD: The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage. BMC Genomics. 2012, 13 (Suppl.3): S1-
PubMed
CAS
PubMed Central
Google Scholar
Hsieh LS, Hsieh YL, Yeh CS, Cheng CY, Yang CC, Lee PD: Molecular characterization of a phenylalanine ammonia-lyase gene (BoPAL1) from B.oldhamii. Mol Biol Rep. 2011, 38: 283-290. 10.1007/s11033-010-0106-2.
Article
PubMed
CAS
Google Scholar
Tan RX, Zou WX: Endophytes: a rich source of functional metabolites. Nat Prod Rep. 2001, 18: 448-459. 10.1039/b100918o.
Article
PubMed
CAS
Google Scholar
Fiona CC, Laurence BD, Norman GL: The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry. 2004, 65: 1557-1564. 10.1016/j.phytochem.2004.05.006.
Article
Google Scholar
Lee SW, Robb J, Nazar RN: Truncated phenylalanine ammonia-lyase expression in tomato (Lycopersicon esculentum). J Biol Chem. 1992, 267: 11824-11830.
PubMed
CAS
Google Scholar
Chaw SM, Zhaekikh A, Sung HM, Lau TC, Li WH: Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol Biol Evol. 1997, 14: 56-68. 10.1093/oxfordjournals.molbev.a025702.
Article
PubMed
CAS
Google Scholar
Keeling PJ, Palmer JD: Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet. 2008, 9: 605-618. 10.1038/nrg2386.
Article
PubMed
CAS
Google Scholar
Bergthorsson U, Adams KL, Thomason B, Palmer JD: Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature. 2003, 424: 197-201. 10.1038/nature01743.
Article
PubMed
CAS
Google Scholar
Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD: Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA. 2004, 101: 17747-17752. 10.1073/pnas.0408336102.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hao W, Richardson AO, Zheng Y, Palmer JD: Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. Proc Natl Acad Sci USA. 2010, 107: 21576-21581. 10.1073/pnas.1016295107.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rumpho ME, Worful JM, Lee J, Kannan K, Tyler MS, Bhattacharya D, Moustafa M, Manhart JR: Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc Natl Acad Sci USA. 2008, 105: 17867-17871. 10.1073/pnas.0804968105.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yang J, Huang JX, Gu HY, Zhong Y, Yang ZH: Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol Biol Evol. 2002, 19: 1752-1759. 10.1093/oxfordjournals.molbev.a003997.
Article
PubMed
CAS
Google Scholar
Kumar A, Ellis BE: The phenylalanine ammonia-lyase gene family in raspberry. Structure, expression, and evolution. Plant Physiol. 2001, 127: 230-239. 10.1104/pp.127.1.230.
Article
PubMed
CAS
PubMed Central
Google Scholar
Röther D, Poppe L, Morlock G, Viergutz S, Rétey J: An active site homology model of phenylalanine ammonia-lyase from Petroselinum crispum. Eur J Biochem. 2002, 269: 3065-3075. 10.1046/j.1432-1033.2002.02984.x.
Article
PubMed
Google Scholar
Allwood EG, Davies DR, Gerrish C, Ellis BE, Bolwell GP: Phosphorylation of phenylalanine ammonia-lyase: evidence for a novel protein kinase and identification of the phosphorylated residue. FEBS Lett. 1999, 457: 47-52. 10.1016/S0014-5793(99)00998-9.
Article
PubMed
CAS
Google Scholar
Xu EY, Moore FL, Reijo Pera RA: A gene family required for human germ cell development evolved from an ancient meiotic gene conserved in all metazoans. Proc Natl Acad Sci USA. 2001, 98: 7414-7419. 10.1073/pnas.131090498.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li JK, Zhou EX, Li DX, Huang SQ: Multiple northern refugia for Asian sacred lotus, an aquatic plant with characteristics of ice-age endurance. Aust J Bot. 2010, 58: 463-472. 10.1071/BT10002.
Article
Google Scholar
Thompson JD, Gibson TJ, Higgins DG: Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. 2002, 00: 2.3.1-2.3.22.
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using likelihood, distance, and parsimony methods. Mol Biol Evol. 2011, 28: 2731-2739. 10.1093/molbev/msr121.
Article
PubMed
CAS
PubMed Central
Google Scholar
Guindon S, Delsuc F, Dufayard JF, Gascuel O: Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol. 2009, 537: 113-137. 10.1007/978-1-59745-251-9_6.
Article
PubMed
CAS
Google Scholar
Huelsenbeck JP, Ronquist F: MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001, 17: 754-755. 10.1093/bioinformatics/17.8.754.
Article
PubMed
CAS
Google Scholar
Gambino G, Perrone I, Gribaudo I: A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal. 2008, 19: 520-525. 10.1002/pca.1078.
Article
PubMed
CAS
Google Scholar
Bradford MM: A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976, 72: 248-254. 10.1016/0003-2697(76)90527-3.
Article
PubMed
CAS
Google Scholar
D’Cunha GB, Satyanarayan S, Nair PM: Purification of phenylalanine ammonia lyase from Rhodotorula glutinis. Phytochemistry. 1996, 42: 17-20. 10.1016/0031-9422(95)00914-0.
Article
Google Scholar