KEGG   PATHWAY: aly00940
Entry
aly00940                    Pathway                                
Name
Phenylpropanoid biosynthesis - Arabidopsis lyrata (lyrate rockcress)
Description
Phenylpropanoids are a group of plant secondary metabolites derived from phenylalanine and having a wide variety of functions both as structural and signaling molecules. Phenylalanine is first converted to cinnamic acid by deamination. It is followed by hydroxylation and frequent methylation to generate coumaric acid and other acids with a phenylpropane (C6-C3) unit. Reduction of the CoA-activated carboxyl groups of these acids results in the corresponding aldehydes and alcohols. The alcohols are called monolignols, the starting compounds for biosynthesis of lignin.
Class
Metabolism; Biosynthesis of other secondary metabolites
Pathway map
aly00940  Phenylpropanoid biosynthesis
aly00940

Module
aly_M00039  Monolignol biosynthesis, phenylalanine/tyrosine => monolignol [PATH:aly00940]
aly_M00137  Flavanone biosynthesis, phenylalanine => naringenin [PATH:aly00940]
Other DBs
GO: 0009699
Organism
Arabidopsis lyrata (lyrate rockcress) [GN:aly]
Gene
9317554  phenylalanine ammonia-lyase 1 [KO:K10775] [EC:4.3.1.24]
9309209  phenylalanine ammonia-lyase 3 [KO:K10775] [EC:4.3.1.24]
9312266  phenylalanine ammonia-lyase 2 [KO:K10775] [EC:4.3.1.24]
9318728  phenylalanine ammonia-lyase 4 isoform X2 [KO:K10775] [EC:4.3.1.24]
9317181  trans-cinnamate 4-monooxygenase [KO:K00487] [EC:1.14.14.91]
9306078  4-coumarate--CoA ligase-like 6 [KO:K01904] [EC:6.2.1.12]
9327714  4-coumarate--CoA ligase 1 [KO:K01904] [EC:6.2.1.12]
9319361  4-coumarate--CoA ligase 4 [KO:K01904] [EC:6.2.1.12]
9308807  4-coumarate--CoA ligase-like 7 [KO:K01904] [EC:6.2.1.12]
9321496  4-coumarate--CoA ligase 2 [KO:K01904] [EC:6.2.1.12]
9322511  LOW QUALITY PROTEIN: 4-coumarate--CoA ligase-like 1 [KO:K01904] [EC:6.2.1.12]
9324368  4-coumarate--CoA ligase 3 [KO:K01904] [EC:6.2.1.12]
9302623  4-coumarate--CoA ligase-like 9 [KO:K01904] [EC:6.2.1.12]
9300608  shikimate O-hydroxycinnamoyltransferase [KO:K13065] [EC:2.3.1.133]
9322309  spermidine hydroxycinnamoyl transferase [KO:K13065] [EC:2.3.1.133]
9327949  shikimate O-hydroxycinnamoyltransferase [KO:K13065] [EC:2.3.1.133]
9315964  cytochrome P450 98A3 [KO:K09754] [EC:1.14.14.96]
9316384  caffeoylshikimate esterase [KO:K18368] [EC:3.1.1.-]
9317721  caffeoylshikimate esterase isoform X1 [KO:K18368] [EC:3.1.1.-]
9314550  caffeoylshikimate esterase [KO:K18368] [EC:3.1.1.-]
9309827  caffeoylshikimate esterase isoform X1 [KO:K18368] [EC:3.1.1.-]
9330463  caffeoylshikimate esterase [KO:K18368] [EC:3.1.1.-]
9325206  caffeoylshikimate esterase [KO:K18368] [EC:3.1.1.-]
9314092  caffeoylshikimate esterase [KO:K18368] [EC:3.1.1.-]
9305249  caffeoyl-CoA O-methyltransferase 1 [KO:K00588] [EC:2.1.1.104]
9324710  putative caffeoyl-CoA O-methyltransferase At1g67980 isoform X1 [KO:K00588] [EC:2.1.1.104]
9326760  putative caffeoyl-CoA O-methyltransferase At1g67980 [KO:K00588] [EC:2.1.1.104]
9305692  probable caffeoyl-CoA O-methyltransferase At4g26220 isoform X2 [KO:K00588] [EC:2.1.1.104]
110224260  cinnamoyl-CoA reductase 2 [KO:K09753] [EC:1.2.1.44]
9326201  cinnamoyl-CoA reductase 1 [KO:K09753] [EC:1.2.1.44]
9319591  aldehyde dehydrogenase family 2 member C4 [KO:K12355] [EC:1.2.1.68]
9304951  cytochrome P450 84A1 [KO:K09755] [EC:1.14.-.-]
9303101  cytochrome P450 84A1 [KO:K09755] [EC:1.14.-.-]
9307157  cytochrome P450 84A4 [KO:K09755] [EC:1.14.-.-]
9303555  flavone 3'-O-methyltransferase 1 [KO:K13066] [EC:2.1.1.68 2.1.1.4]
9303558  flavone 3'-O-methyltransferase 1 [KO:K13066] [EC:2.1.1.68 2.1.1.4]
9302099  flavone 3'-O-methyltransferase 1 [KO:K13066] [EC:2.1.1.68 2.1.1.4]
9302094  flavone 3'-O-methyltransferase 1 [KO:K13066] [EC:2.1.1.68 2.1.1.4]
9305026  cinnamyl alcohol dehydrogenase 7 [KO:K00083] [EC:1.1.1.195]
9305024  cinnamyl alcohol dehydrogenase 8 [KO:K00083] [EC:1.1.1.195]
9302914  probable cinnamyl alcohol dehydrogenase 9 [KO:K00083] [EC:1.1.1.195]
9305236  cinnamyl alcohol dehydrogenase 5 [KO:K00083] [EC:1.1.1.195]
9316464  cinnamyl alcohol dehydrogenase 3 isoform X1 [KO:K00083] [EC:1.1.1.195]
9319250  cinnamyl alcohol dehydrogenase 4 [KO:K00083] [EC:1.1.1.195]
9324951  probable cinnamyl alcohol dehydrogenase 1 [KO:K00083] [EC:1.1.1.195]
9305027  probable cinnamyl alcohol dehydrogenase 6 isoform X1 [KO:K00083] [EC:1.1.1.195]
9326958  berberine bridge enzyme-like 13 [KO:K22395] [EC:1.1.1.195]
9315583  berberine bridge enzyme-like 15 [KO:K22395] [EC:1.1.1.195]
9330158  1-Cys peroxiredoxin PER1 [KO:K11188] [EC:1.11.1.7 1.11.1.27 3.1.1.-]
9312012  peroxidase 33 [KO:K00430] [EC:1.11.1.7]
110228651  peroxidase 67 [KO:K00430] [EC:1.11.1.7]
110229111  peroxidase 20 [KO:K00430] [EC:1.11.1.7]
9313161  peroxidase 31 [KO:K00430] [EC:1.11.1.7]
9312016  peroxidase 34 [KO:K00430] [EC:1.11.1.7]
9323275  peroxidase 11 [KO:K00430] [EC:1.11.1.7]
110228869  peroxidase 22 [KO:K00430] [EC:1.11.1.7]
110228125  peroxidase 72 [KO:K00430] [EC:1.11.1.7]
9314682  peroxidase 17 [KO:K00430] [EC:1.11.1.7]
9322216  peroxidase 15 [KO:K00430] [EC:1.11.1.7]
9303352  peroxidase 46 [KO:K00430] [EC:1.11.1.7]
9321253  peroxidase 29 [KO:K00430] [EC:1.11.1.7]
9306844  peroxidase 62 [KO:K00430] [EC:1.11.1.7]
9305923  peroxidase 42 [KO:K00430] [EC:1.11.1.7]
9325186  peroxidase 13 [KO:K00430] [EC:1.11.1.7]
9328878  peroxidase 4 [KO:K00430] [EC:1.11.1.7]
110226673  peroxidase 49 [KO:K00430] [EC:1.11.1.7]
9305055  peroxidase 50 [KO:K00430] [EC:1.11.1.7]
9327368  peroxidase 9 [KO:K00430] [EC:1.11.1.7]
9317657  peroxidase 23 [KO:K00430] [EC:1.11.1.7]
9317557  peroxidase 21 [KO:K00430] [EC:1.11.1.7]
9319386  peroxidase 30 [KO:K00430] [EC:1.11.1.7]
9309343  peroxidase 53 [KO:K00430] [EC:1.11.1.7]
9324906  peroxidase 12 [KO:K00430] [EC:1.11.1.7]
9315849  peroxidase 24 [KO:K00430] [EC:1.11.1.7]
9325605  peroxidase 2 [KO:K00430] [EC:1.11.1.7]
9327583  peroxidase 10 [KO:K00430] [EC:1.11.1.7]
110227125  peroxidase 58 [KO:K00430] [EC:1.11.1.7]
110227190  peroxidase 54 [KO:K00430] [EC:1.11.1.7]
9303255  peroxidase 47 [KO:K00430] [EC:1.11.1.7]
9325606  peroxidase 2 [KO:K00430] [EC:1.11.1.7]
9328339  peroxidase 3 [KO:K00430] [EC:1.11.1.7]
9306794  peroxidase 63 [KO:K00430] [EC:1.11.1.7]
9305463  peroxidase 45 [KO:K00430] [EC:1.11.1.7]
9303657  peroxidase 44 [KO:K00430] [EC:1.11.1.7]
9305705  peroxidase 44 [KO:K00430] [EC:1.11.1.7]
9303658  peroxidase 43 [KO:K00430] [EC:1.11.1.7]
9304217  peroxidase 40 [KO:K00430] [EC:1.11.1.7]
9316114  probable peroxidase 26 [KO:K00430] [EC:1.11.1.7]
9317844  peroxidase 25 [KO:K00430] [EC:1.11.1.7]
9325183  peroxidase 13 [KO:K00430] [EC:1.11.1.7]
9309780  peroxidase 56 [KO:K00430] [EC:1.11.1.7]
9307722  peroxidase 56 [KO:K00430] [EC:1.11.1.7]
9310621  peroxidase 38 [KO:K00430] [EC:1.11.1.7]
9308483  peroxidase 37 [KO:K00430] [EC:1.11.1.7]
9309275  peroxidase 52 [KO:K00430] [EC:1.11.1.7]
9310137  peroxidase 60 [KO:K00430] [EC:1.11.1.7]
9308640  peroxidase 39 [KO:K00430] [EC:1.11.1.7]
9311634  peroxidase 32 [KO:K00430] [EC:1.11.1.7]
9312076  peroxidase 35 [KO:K00430] [EC:1.11.1.7]
9310232  probable peroxidase 61 [KO:K00430] [EC:1.11.1.7]
9308482  peroxidase 37 [KO:K00430] [EC:1.11.1.7]
9305262  putative Peroxidase 48 [KO:K00430] [EC:1.11.1.7]
9304118  peroxidase 41 [KO:K00430] [EC:1.11.1.7]
9312131  peroxidase 36 [KO:K00430] [EC:1.11.1.7]
9307980  peroxidase 59 [KO:K00430] [EC:1.11.1.7]
9307672  peroxidase 55 [KO:K00430] [EC:1.11.1.7]
9308348  peroxidase 34 [KO:K00430] [EC:1.11.1.7]
9318261  peroxidase 27 [KO:K00430] [EC:1.11.1.7]
9320246  peroxidase 16 [KO:K00430] [EC:1.11.1.7]
9328879  peroxidase 5 [KO:K00430] [EC:1.11.1.7]
9309923  peroxidase 57 [KO:K00430] [EC:1.11.1.7]
9301226  peroxidase 65 [KO:K00430] [EC:1.11.1.7]
9298481  peroxidase 70 [KO:K00430] [EC:1.11.1.7]
9320470  peroxidase 28 [KO:K00430] [EC:1.11.1.7]
9299891  peroxidase 64 [KO:K00430] [EC:1.11.1.7]
9328338  peroxidase 2 [KO:K00430] [EC:1.11.1.7]
9314869  peroxidase 18 [KO:K00430] [EC:1.11.1.7]
9329387  peroxidase 6 [KO:K00430] [EC:1.11.1.7]
9300215  peroxidase 66 [KO:K00430] [EC:1.11.1.7]
9300960  peroxidase 69 [KO:K00430] [EC:1.11.1.7]
9302667  peroxidase 70 [KO:K00430] [EC:1.11.1.7]
9302668  peroxidase 71 [KO:K00430] [EC:1.11.1.7]
9301080  peroxidase 73 [KO:K00430] [EC:1.11.1.7]
9329714  peroxidase 7 [KO:K00430] [EC:1.11.1.7]
9313833  UDP-glycosyltransferase 72E1 [KO:K12356] [EC:2.4.1.111]
9302818  UDP-glycosyltransferase 72E3 [KO:K12356] [EC:2.4.1.111]
9322250  UDP-glycosyltransferase 72D1 [KO:K12356] [EC:2.4.1.111]
9314717  serine carboxypeptidase-like 8 [KO:K09757] [EC:3.4.16.- 2.3.1.92]
9325047  cytochrome P450 98A8 [KO:K15506] [EC:1.14.13.-]
9323610  cytochrome P450 98A9 [KO:K23662] [EC:1.14.13.-]
9324709  tapetum-specific methyltransferase 1 [KO:K13067] [EC:2.1.1.-]
Compound
C00079  L-Phenylalanine
C00082  L-Tyrosine
C00223  p-Coumaroyl-CoA
C00315  Spermidine
C00323  Caffeoyl-CoA
C00406  Feruloyl-CoA
C00411  Sinapoyl-CoA
C00423  trans-Cinnamate
C00482  Sinapate
C00540  Cinnamoyl-CoA
C00590  Coniferyl alcohol
C00761  Coniferin
C00811  4-Coumarate
C00852  Chlorogenate
C00903  Cinnamaldehyde
C00933  Sinapine
C01175  1-O-Sinapoyl-beta-D-glucose
C01197  Caffeate
C01494  Ferulate
C01533  Syringin
C02325  Sinapyl alcohol
C02646  4-Coumaryl alcohol
C02666  Coniferyl aldehyde
C02887  Sinapoyl malate
C02947  4-Coumaroylshikimate
C04366  3-(2-Carboxyethenyl)-cis,cis-muconate
C05608  4-Hydroxycinnamyl aldehyde
C05610  Sinapoyl aldehyde
C05619  5-Hydroxyferulic acid
C05627  4-Hydroxystyrene
C05855  4-Hydroxycinnamyl alcohol 4-D-glucoside
C06224  3,4-Dihydroxystyrene
C10428  Anethole
C10434  5-O-Caffeoylshikimic acid
C10452  Estragole
C10453  Eugenol
C10454  Methyleugenol
C10469  Isoeugenol
C10478  Methylisoeugenol
C10945  Caffeic aldehyde
C12203  5-Hydroxyferuloyl-CoA
C12204  5-Hydroxyconiferaldehyde
C12205  5-Hydroxyconiferyl alcohol
C12206  Caffeyl alcohol
C12208  p-Coumaroyl quinic acid
C15804  p-Hydroxyphenyl lignin
C15805  Guaiacyl lignin
C15806  Syringyl lignin
C15807  5-Hydroxy-guaiacyl lignin
C16930  Chavicol
C18069  N1,N5,N10-Tricoumaroyl spermidine
C18070  N1,N5,N10-Tricaffeoyl spermidine
C18071  N1,N5,N10-Triferuloyl spermidine
C18072  N1,N5,N10-Tri(hydroxyferuloyl) spermidine
C18073  N1,N5-Di(hydroxyferuloyl)-N10-sinapoyl spermidine
C20225  Coniferyl acetate
C20464  Isochavicol
C20465  Coumaryl acetate
Reference
  Authors
Nair RB, Bastress KL, Ruegger MO, Denault JW, Chapple C.
  Title
The Arabidopsis thaliana REDUCED EPIDERMAL FLUORESCENCE1 gene encodes an aldehyde dehydrogenase involved in ferulic acid and sinapic acid biosynthesis.
  Journal
Plant Cell 16:544-54 (2004)
DOI:10.1105/tpc.017509
Reference
  Authors
Baucher M, Halpin C, Petit-Conil M, Boerjan W.
  Title
Lignin: genetic engineering and impact on pulping.
  Journal
Crit Rev Biochem Mol Biol 38:305-50 (2003)
DOI:10.1080/10409230391036757
Reference
  Authors
Rogers LA, Dubos C, Cullis IF, Surman C, Poole M, Willment J, Mansfield SD, Campbell MM.
  Title
Light, the circadian clock, and sugar perception in the control of lignin biosynthesis.
  Journal
J Exp Bot 56:1651-63 (2005)
DOI:10.1093/jxb/eri162
Reference
  Authors
Whetten R, Sederoff R.
  Title
Lignin Biosynthesis.
  Journal
Plant Cell 7:1001-1013 (1995)
DOI:10.1105/tpc.7.7.1001
Reference
PMID:8972602
  Authors
Lorenzen M, Racicot V, Strack D, Chapple C.
  Title
Sinapic acid ester metabolism in wild type and a sinapoylglucose-accumulating mutant of arabidopsis.
  Journal
Plant Physiol 112:1625-30 (1996)
DOI:10.1104/pp.112.4.1625
Reference
PMID:1477555
  Authors
Chapple CC, Vogt T, Ellis BE, Somerville CR.
  Title
An Arabidopsis mutant defective in the general phenylpropanoid pathway.
  Journal
Plant Cell 4:1413-24 (1992)
DOI:10.1105/tpc.4.11.1413
Reference
  Authors
Raes J, Rohde A, Christensen JH, Van de Peer Y, Boerjan W.
  Title
Genome-wide characterization of the lignification toolbox in Arabidopsis.
  Journal
Plant Physiol 133:1051-71 (2003)
DOI:10.1104/pp.103.026484
Reference
  Authors
Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG.
  Title
An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof.
  Journal
Phytochemistry 64:1097-112 (2003)
DOI:10.1016/S0031-9422(03)00517-X
Reference
  Authors
Meyermans H, Morreel K, Lapierre C, Pollet B, De Bruyn A, Busson R, Herdewijn P, Devreese B, Van Beeumen J, Marita JM, Ralph J, Chen C, Burggraeve B, Van Montagu M, Messens E, Boerjan W.
  Title
Modifications in lignin and accumulation of phenolic glucosides in poplar xylem upon down-regulation of caffeoyl-coenzyme A O-methyltransferase, an enzyme involved in lignin biosynthesis.
  Journal
J Biol Chem 275:36899-909 (2000)
DOI:10.1074/jbc.M006915200
Reference
  Authors
Gachon CM, Langlois-Meurinne M, Henry Y, Saindrenan P.
  Title
Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications.
  Journal
Plant Mol Biol 58:229-45 (2005)
DOI:10.1007/s11103-005-5346-5
Reference
  Authors
Li L, Popko JL, Umezawa T, Chiang VL.
  Title
5-hydroxyconiferyl aldehyde modulates enzymatic methylation for syringyl monolignol formation, a new view of monolignol biosynthesis in angiosperms.
  Journal
J Biol Chem 275:6537-45 (2000)
DOI:10.1074/jbc.275.9.6537
Reference
  Authors
Yamauchi K, Yasuda S, Fukushima K.
  Title
Evidence for the biosynthetic pathway from sinapic acid to syringyl lignin using labeled sinapic acid with stable isotope at both methoxy groups in Robinia pseudoacacia and Nerium indicum.
  Journal
J Agric Food Chem 50:3222-7 (2002)
DOI:10.1021/jf011565x
Reference
  Authors
Eckardt NA.
  Title
Probing the mysteries of lignin biosynthesis: the crystal structure of caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase provides new insights.
  Journal
Plant Cell 14:1185-9 (2002)
DOI:10.1105/tpc.140610
Related
pathway
aly00130  Ubiquinone and other terpenoid-quinone biosynthesis
aly00400  Phenylalanine, tyrosine and tryptophan biosynthesis
aly00941  Flavonoid biosynthesis
aly00945  Stilbenoid, diarylheptanoid and gingerol biosynthesis
KO pathway
ko00940   
LinkDB

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