Tables

Table 1

A thaliana PAL gene under investigation in this project.

WSU IDChromosomeChromosome LocusClone LocusProtein Acc #mRNA
Atpal12At2g37040T1J8.22AAP59438AY303128
Atpal43At3g10340F14P13.6AAP59440AY303130
Atpal23At3g53260T4D2.190AAP59439AY303129
Atpal35At5g04230F21E1.150N/AAY528562

Table 2

Summary of isolated A. thaliana PAL cDNAs and progress toward characterizing the heterologously expressed proteins.

GeneWSU #cDNA SourceExpression VectorTransformation (E. coli strains)Purified to HomogeneityPAL activity
At2g37040Atpal1ABRCpET Blue-1Tuner (DE3pLacI)++
At3g10340Atpal4PlantpET Blue-1Tuner (DE3pLacI)++
At3g53260Atpal2PlantpET Blue-1Tuner (DE3pLacI)++
At5g04230Atpal3*PlantTuner (DE3pLacI)++

*Entire plant was used for RNA extraction

Table 3

Summary of isolated A. thaliana PAL promoters and progress toward identifying temporal and spatial patterns of expression

Gene WSU #PCR4 vectorPCambia 1305.1Agrobacterium tumefaciensArabidopsis transformation
At2g37040Atpal1++++
At3g10340Atpal4++++
At3g10340Atpal4++++
At3g53260Atpal2++++
At5g04230Atpal3++++

Table 4

A thaliana 4CL gene under investigation in this project.

WSU IDChromosomeChromosome LocusChromosome LocusProtein Acc #mRNA
At4CL11At1g51680F19C24.11AAQ86588AY376729
At4CL23At3g21240MXL8.10AAQ86587AY376728
At4CL31At1g65060F16G16.6AAQ86589AY376730
At4CL45At5g63380K9H21.11AAQ86590AY376731
At4CL53At3g21230MXL8.9AAQ86591AY376732
At4CL64At4g05160C6L9.15
C17L7.80
AAM67483AY122950
At4CL74At4g19010F13C5.180AAQ86592AY376733
At4CL83At3g48990T2J13.170AAA61449AY117254
At4CL91At1g20510F5M15.17AAK64105AY040047
At4CL101At1g62940F16P17.9AAQ86593AY376734
At4CL115At5g38120F16F17.12 MXA21.2AAQ86594AY376735

Table 5

Summary of isolated A. thaliana 4CL cDNAs and progress toward characterizing the heterologously expressed proteins.

GeneWSU #cDNA SourceCloning in TOPO TAExpression Vector (pCRT7-CT)Transformation (E. coli strains)Purified to Homogeneity4CL Activity
At1g51680At4CL1whole plant+++++
At3g21240At4CL2whole plant+++++
At1g65060At4CL3whole plant++++
At5g63380At4CL4whole plant++++nd
At3g21230At4CL5whole plant+++++
At4g05160At4CL6ABRC
(U19441)
++++nd
At4g19010At4CL7whole plant++++nd
At3g48990At4CL8ABRC
(U11110)
++++nd
At1g20510At4CL9ABRC
(U09223)
++++nd
At1g62940At4CL10whole plant+++++
At5g38120At4CL11whole plant++++nd

Table 6

Summary of isolated A. thaliana 4CL promoters and progress toward identifying temporal and spatial patterns of expression.

GeneWSU #PCR4 vectorpCambia
1305.1
Agrobacterium tumefaciensArabidopsis transformation
At1g51680At4CL1++++
At3g21240At4CL2++++
At1g65060At4CL3++++
At5g63380At4CL4++++
At3g21230At4CL5++++
At4g05160At4CL6++++
At4g19010At4CL7++++
At3g48990At4CL8++++
At1g20510At4CL9++++
At1g62940At4CL10++++
At5g38120At4CL11++++

Table 7

A thaliana CCOMT gene under investigation in this project.

WSU #Chromosome
Chromosome locusClone locus
AtCCOMT14At4g34050F28A23.190
AtCCOMT24At4g26220T25K17.30
AtCCOMT31At1g67990T23K23.16
AtCCOMT41At1g67980T23K23.17
AtCCOMT51At1g24735
F5A9.20

Table 8

Summary of isolated A. thaliana CCOMT cDNAs and progress toward characterizing the heterologously expressed proteins.

GeneWSU #cDNA sourceCloning vectorTransformation
(E.coli strain)
Expression strain
At4g34050AtCCOMT1RNA from 2-week seedlingspET-101
pET-151
TOP-10
TOP-10
N/A
At4g26220AtCCOMT2RNA from 2-week seedlingspET-101
pET-151
pET-44
TOP-10
TOP-10
Novablue
BL21-Star
At1g67990AtCCOMT3RNA from 2-week seedlingspET-151TOP-10N/A
At1g67980AtCCOMT4RNA from 2-week seedlingspET-151TOP-10BL21-Star
At1g24735AtCCOMT5RNA from 2-week seedlingspET-151TOP-10N/A

Table 9

A thaliana COMT gene under investigation in this project.

WSU #ChromosomeChromosome locusClone locus
AtCOMT11At5g54160K18G13.3
AtCOMT21At1g51990F5F19.5
AtCOMT35At5g53810MGN6.20
AtCOMT43At3g53140T4D2.70
AtCOMT55At5g37170MJG14.10
AtCOMT61At1g63140F16M19.12
AtCOMT71At1g77520T5M16.11
AtCOMT81At1g21130T22I11.4
AtCOMT91At1g77530T5M16.12
AtCOMT101At1g33030F9L11.18
AtCOMT111At1g21100T22I11.7
AtCOMT121At1g21120T22I11.5
AtCOMT131At1g21110T22I11.6
AtCOMT141At1g62900F16P17.4
AtCOMT151At1g76790F28O16.16
AtCOMT164At4g35150T12J5.20
AtCOMT174At4g35160T12J5.30

Table 10

Summary of isolated A. thaliana COMT cDNAs and progress toward characterizing the heterologously expressed proteins.

GeneWSU #cDNA SourceExpression VectorTransformation (E. coli strains)Purified to HomogeneityCOMT Activity
At5g54160AtCOMT1PlantpEt101+++
At1g51990AtCOMT2PlantpEt101++-
At5g53810AtCOMT3ABRCpEt101++-
At3g53140AtCOMT4PlantpEt101++-
At5g37170AtCOMT5PlantpEt101++-
At1g63140AtCOMT6PlantpEt101++-
At1g77520AtCOMT7PlantpEt101++-
At1g21130AtCOMT8PlantpEt101++-
At1g77530AtCOMT9PlantpEt101++-
At1g33030AtCOMT10PlantpEt101++-
At1g21100AtCOMT11PlantpEt101++-
At1g21120AtCOMT12PlantpEt101++-
At1g21110AtCOMT13PlantpEt101++-
At1g62900AtCOMT14PlantpEt101++-
At1g76790AtCOMT15PlantpEt101++-
At4g35150AtCOMT16PlantpEt101++-
At4g35160AtCOMT17PlantpEt101++-

Table 11

A thaliana CCR gene under investigation in this project.

WSU IDChromosomeChromosome LocusClone Locus
Atccr11At1g15950T24D18.5
Atccr131At1g66800F4N21.7
Atccr41At1g68540T26J14.11
Atccr9/101At1g76470F14G6.7
Atccr21At1g80820F23A5.17
Atccr32At2g02400T16F16.19
Atccr62At2g23910T29E15.11
Atccr82At2g33590F4P9.36
Atccr112At2g33600F4P9.37
Atccr74At4g30470F17I23.190
Atccr55At5g14700T15N1.190
Atccr5a5At5g14700T15N1.190
Atccr125At5g58490MQJ2.6

Table 12

Summary of isolated A. thaliana CCR cDNAs and progress toward characterizing the heterologously expressed proteins.

GeneWSU #cDNA SourceExpression VectorTransformation (E. coli strains)Purified to HomogeneityCCR Activity
At1g15950Atccr1PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)
BL21*
++
At1g80820Atccr2ABRCpET Blue-1
pCRT7/CT TOPO
++
At2g02400Atccr3PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)+-
At1g68540Atccr4PlantpET Blue-1
pET101/D
Tuner (DE3pLacI)N/AN/A
At5g14700Atccr5PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)
BL21*
N/AN/A
At5g14700Atccr5aPlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)N/AN/A
At2g23910Atccr6PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)N/AN/A
At4g30470Atccr7PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)N/AN/A
At2g33590Atccr8PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)N/AN/A
At1g76470Atccr9/10PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)N/AN/A
At2g33600Atccr11PlantpET Blue-1
pCRT7/CT TOPO
Tuner (DE3pLacI)N/AN/A
At5g58490Atccr12N/AN/AN/AN/AN/A
At1g66800Atccr13N/AN/AN/AN/AN/A

Table 13

 Summary of isolated A. thaliana CCR promoters and progress toward identifying temporal and spatial patterns of expression.

GeneWSU #PCR4 vectorpCambia
1305.1
Agrobacterium tumefaciensArabidopsis transformation
At1g15950Atccr1++++
At1g80820Atccr2+N/AN/AN/A
At2g02400Atccr3++++
At1g68540Atccr4N/AN/AN/AN/A
At5g14700Atccr5+N/AN/AN/A
At5g14700Atccr5aN/AN/AN/AN/A
At2g23910Atccr6+N/AN/AN/A
At4g30470Atccr7N/AN/AN/AN/A
At2g33590Atccr8++N/AN/A
At1g76470Atccr9/10+N/AN/AN/A
At2g33600Atccr11++N/AN/A
At5g58490Atccr12++++
At1g66800Atccr13N/AN/AN/AN/A

Table 14

 A thaliana CAD gene under investigation in this project.

WSU #ChromosomeChromosome
Locus
Clone LocusProtein Acc #mRNA Acc #
AtCAD11At1g72680F28P22.13AAP40269AY288079
AtCAD2
2At2g21730F7D8.5AAP59430AY302077
AtCAD32At2g21890F7D8.21AAP59431AY302078
AtCAD4
3At3g19450MLD14.30AAP59434AY302081
AtCAD5
4At4g34230F10M10.11/
F28A23.10
AAP59435AY302082
AtCAD6
4At4g37970F20D10.90AAP59428AY302075
AtCAD7
4At4g37980F20D10.100AAP59432AY302079
AtCAD8
4At4g37990F20D10.110AAP59433AY302080
AtCAD9
4At4g39330T22F8.230AAP59429AY302076

Table 15

Summary of isolated A. thaliana CAD cDNAs and progress toward characterizing the heterologously expressed proteins.

GeneWSU #CDNA sourceExpression
Vector
cloning
Transformation
(E. coli strain)
Purified to
Homogeneity
At1g72680AtCAD1Leaves, Stems,
and Siliques
pET101/D-TOPOTuner(DE3)+
At2g21730AtCAD2Leaves, Stems,
and Siliques
pET101/D-TOPOTuner(DE3)+
At2g21890AtCAD3Leaves, Stems,
and Siliques
pET101/D-TOPOTuner(DE3)+
At3g19450AtCAD4Leaves, Stems,
and Siliques
pTrcHis2-TOPOTOP10+
At4g34230AtCAD5Leaves, Stems,
and Siliques
pTrcHis2-TOPOTOP10+
4g37970AtCAD6Leaves, Stems,
and Siliques
pET101/D-TOPOTuner(DE3)+
At4g37980AtCAD7Leaves, Stems,
and Siliques
pTrcHis2-TOPOTOP10+
At4g37990AtCAD8Leaves, Stems,
and Siliques
pTrcHis2-TOPOTOP10+
At4g39330AtCAD9Leaves, Stems,
and Siliques
pET101/D-TOPOTuner(DE3)+

Table 16

Kinetic parameters for CAD homologues, AtCAD2 – 5, 7 and 8.

WSU IDSubstrateKm
(µM)
Vmax
(pKat/µg)
kcat
(sec–1)
kenz
(M–1 sec–1)
AtCAD4p-Coumaryl aldehyde4744.03.4474,000
AtCAD4Caffeyl aldehyde8717.11.3315,000
AtCAD4Coniferyl aldehyde6526.82.1032,000
AtCAD45-OH Coniferyl aldehyde8532.32.5230,000
AtCAD4Sinapyl aldehyde2749.20.722,600
ATCAD5p-Coumaryl aldehyde13187.314.521,091,000
ATCAD5Caffeyl aldehyde6894.17.30107,000
ATCAD5Coniferyl aldehyde35157.412.19348,000
ATCAD55-OH Coniferyl aldehyde22106.98.28370,000
ATCAD5Sinapyl aldehyde20177.013.72700,000
ATCAD2p-Coumaryl aldehyde1143.30.272,400
ATCAD2Caffeyl aldehyde16122.21.8111,000
ATCAD2Coniferyl aldehyde4528.00.651,400
ATCAD25-OH Coniferyl aldehyde33616.41.344,000
ATCAD2Sinapyl aldehyde2,16148.13.931,800
ATCAD3p-Coumaryl aldehyde29220.11.655,600
ATCAD3Caffeyl aldehyde5819.70.801,400
ATCAD3Coniferyl aldehyde3624.80.391,100
ATCAD35-OH Coniferyl aldehyde53417.91.472,800
ATCAD3Sinapyl aldehyde6299.10.741,200
ATCAD7p-Coumaryl aldehyde32028.62.186,800
ATCAD7Caffeyl aldehyde3,68579.06.041,600
ATCAD7Coniferyl aldehyde67513.00.991,500
ATCAD75-OH Coniferyl aldehyde7562.70.21280
ATCAD7Sinapyl aldehyde3030.60.05150
ATCAD8p-Coumaryl aldehyde30220.41.595,300
ATCAD8Caffeyl aldehyde6837.00.54800
ATCAD8Coniferyl aldehyde1415.60.443,100
ATCAD85-OH Coniferyl aldehyde45710.40.811,800
ATCAD8Sinapyl aldehyde89828.92.252,500

Table 17

Summary of isolated A. thaliana CAD promoters and progress toward identifying temporal and spatial patterns of expression.

GeneWSU #PCR4 vectorpCambia
1305.1
Agrobacterium tumefaciensArabidopsis transformationAnalysis of T2 plants
At1g72680AtCAD1+++++
At2g21730AtCAD2++++-
At2g21890AtCAD3+++++
At3g19450AtCAD4+++++
At4g34230AtCAD5+++++
At4g34230AtCAD5+++++
At4g34230AtCAD5+++++
At4g34230AtCAD5+++++
At4g37970AtCAD6++++-
At4g37980AtCAD7++++-
At4g37990AtCAD8+++++
At4g39330AtCAD9+++++

Table 18

A thaliana APDBR gene under investigation in this project.

WSU #ChromosomeChromosome
Locus
Clone Locus
AtAPDBR91At1g65560F5I14.9
AtAPDBR53At3g03080T17B22.23
AtAPDBR83At3g59845F24G16.1
AtAPDBR15At5g16970F2K13.120
AtAPDBR25At5g16990F2K13.140
AtAPDBR35At5g17000F2K13.150
AtAPDBR45At5g16980F2K13.130
AtAPDBR65At5g38000K18L3.2
/ K19A23.1
AtAPDBR6-1
5At5g37940K18L3.100
F2K13.1105At5g16960F2K13.110
AtAPDBR105At5g37980K18L3.140

Table 19

Summary of isolated A. thaliana APDBR cDNAs and progress toward characterizing the heterologously expressed proteins.

GeneWSU #cDNA sourceExpression
Vector
Transformation
(E. coli strain)
Purified to
Homogeneity
APDBR
Activity
At1g16970AtAPDBR 1Leaves, Stems,
and Siliques
+TOP10++
At2g16990AtAPDBR 2Leaves, Stems,
and Siliques
+TOP10+-
At2g17000AtAPDBR 3Leaves, Stems,
and Siliques
+TOP10+-
At3g16980AtAPDBR 4+TOP10+-
At4g03080AtAPDBR 5Leaves, Stems,
and Siliques
UnderwayN/AN/AN/A
At4g38000AtAPDBR 6Leaves, Stems,
and Siliques
+Tuner(DE3)UnderwayUnderway
At4g37940AtAPDBR 6-1Leaves, Stems,
and Siliques
+Tuner(DE3)UnderwayUnderway
At4g16960AtAPDBR 7Leaves, Stems,
and Siliques
+Tuner(DE3)UnderwayUnderway
At4g59845AtAPDBR 8Leaves, Stems,
and Siliques
+TOP10++
At4g65560AtAPDBR 9Leaves, Stems,
and Siliques
+TOP10++
At4g37980AtAPDBR 10Leaves, Stems,
and Siliques
+TOP10+-

Table 20

Summary of isolated A. thaliana APBDR promoters and progress toward identifying temporal and spatial patterns of expression.

GeneWSU #PCR4 vectorpCambia
1305.1
Agrobacterium tumefaciensArabidopsis transformation
At1g16970AtAPDBR 1++++
At2g16990AtAPDBR 2++++
At2g17000AtAPDBR 3++++
At3g16980AtAPDBR 4++--
At4g03080AtAPDBR 5++++
At4g38000AtAPDBR 6++--
At4g37940AtAPDBR 6-1++--
At4g16960AtAPDBR 7++++
At4g59845AtAPDBR 8++++
At4g65560AtAPDBR 9++++
At4g37980AtAPDBR 10++++

Table 21

A thaliana DIR gene under investigation in this project.

WSU #ChromosomeChromosome
Locus
Clone Locus
ATDIR15At5g42510MDH9.21
ATDIR25At5g42500MDH9.20
ATDIR35At5g49040K19E20.19
ATDIR42At2g21110F26H11.13
ATDIR51At1g64160F22C12.8
ATDIR64At4g23690F9D16.160
ATDIR73At3g13650MMM17.15
ATDIR83At3g13662MMM17.6
ATDIR92At2g39430F12L6.9
ATDIR102At2g28670T8O18.4
ATDIR111At4g38700F19G10.14
ATDIR124At4g11180T22B4.160
ATDIR134At4g11190T22B4.170
ATDIR14/164At4g11210T22B4.190 F8L21.1
ATDIR154At4g38700T9A14.4
F20M13.260
ATDIR184At4g13580
T6G15.130

Table 22

Summary of sense and antisense AtDIR plants.

GeneWSU #Sense (S)/
Antisense (AS) Construct
T0 seedsT1 seedsT2 seedsT3 plants for analysis
At5g42510ATDIR1S+N/AN/AN/A
At5g42510ATDIR1AS++N/A
At5g42500ATDIR2S+++
At5g42500ATDIR2AS+++N/A
At5g49040ATDIR3S+N/A
At5g49040ATDIR3AS++N/AN/A
At2g21110ATDIR4S+++N/A
At2g21110ATDIR4AS+++N/A
At1g64160ATDIR5S++++
At1g64160ATDIR5AS++++
At4g23690ATDIR6S++N/AN/A
At4g23690ATDIR6AS+++N/A
At3g13650ATDIR7S++N/AN/A
At3g13650ATDIR7AS+N/AN/AN/A
At3g13662ATDIR8S+++N/A
At3g13662ATDIR8AS+N/AN/AN/A
At2g39430ATDIR9S++++
At2g39430ATDIR9AS++++
At2g28670ATDIR10S++N/AN/A
At2g28670ATDIR10AS++++
At1g22900ATDIR11S+N/AN/AN/A
At1g22900ATDIR11AS++N/AN/A
At4g11180ATDIR12S++N/AN/A
At4g11180ATDIR12AS++N/AN/A
At4g11190ATDIR13S+++N/A
At4g11190ATDIR13AS+++N/A
At4g11210ATDIR14/16S++++
At4g112101ATDIR14/16AS++++
At4g38700ATDIR15S+N/AN/AN/A
At4g38700ATDIR15AS++N/AN/A
At4g13580ATDIR18S++++
At4g13580ATDIR18AS++N/AN/A

Table 23

Summary of isolated A. thaliana PER cDNAs and progress toward characterizing the heterologously expressed proteins.

WSU # GenecDNA sourceExpression vector
AtPER1At5g1782030 d rootpIB
AtPER2At3g0367014 d whole plantspIB
AtPER3At4g26010ABRCpMT
AtPER4At5g06720N/AN/A
AtPER5At4g11290ABRCN/A
AtPER6At5g22410ABRCN/A
AtPER7At5g64100ABRCpMT
AtPER8At5g39590
N/ApMT
AtPER9At1g0526030 d rootpIB
AtPER10At5g0673030 d rootpIB/ pMT
AtPER11At1g34330N/AN/A
AtPER12At3g32980ABRCN/A
AtPER13aAt2g18980ABRCN/A
AtPER13bAt1g71695ABRCN/A
AtPER14At3g49960N/AN/A
AtPER15aAt1g49660N/ApIB/ pMT
AtPER15b
At3g48690N/AN/A
AtPER16At3g21770ABRCN/A
AtPER17At5g19890ABRCN/A
AtPER19At5g40150N/AN/A
AtPER20At2g3538030 d rootpIB
AtPER21At4g17690N/AN/A
AtPER22At4g16270N/AN/A
AtPER23At4g33870N/AN/A
AtPER24At3g17070N/AN/A
AtPER25At2g34060N/AN/A
AtPER26At2g37130ABRCN/A
AtPER27At1g05250ABRCN/A
AtPER28At5g64120ABRCN/A
AtPER29At5g67400N/AN/A
AtPER30At5g14130ABRCN/A
AtPER31At1g14480N/AN/A
AtPER32At4g31760N/AN/A
AtPER33At3g50990
N/AN/A
AtPER34At2g4148030 d rootpMT
AtPER35
At5g2407030 d rootpMT/pIB
AtPER36At5g58400N/AN/A
AtPER37
At2g38390N/AN/A
AtPER38At2g38380
ABRCN/A
AtPER39At4g3752030 d rootpIB
pIB
AtPER40At4g3017030 d rootN/A
AtPER41
At5g66390N/AN/A
AtPER42At1g68850N/AN/A
AtPER43At4g08770ABRCN/A
AtPER44At1g44970N/AN/A
AtPER45At2g22420N/AN/A
AtPER46At4g3342030 d rootpIB
AtPER47At5g64110N/AN/A
AtPER48At5g5839030 d rootpIB
AtPER49At5g05340N/AN/A
AtPER50At1g24110N/AN/A
AtPER51At1g1449030 d rootpIB
AtPER52At2g43480ABRCN/A
AtPER53At4g21960ABRCN/A
AtPER54At3g49120ABRCN/A
AtPER55At3g49110N/AN/A
AtPER56At5g42180ABRCN/A
AtPER57At3g0119030 d rootpIB
AtPER58At5g51890ABRCN/A
AtPER59At1g30870N/AN/A
AtPER60At3g28200N/AN/A
N/AAt2g18140AtPER61N/A
AtPER62At4g36430ABRCN/A
AtPER63At5g47000N/AN/A
AtPER64At5g15180ABRCN/A
AtPER65At2g39040N/AN/A
AtPER66At1g77100N/AN/A
AtPER67At2g24800N/AN/A
AtPER68At1g34510N/AN/A
AtPER69At5g19880N/AN/A
AtPER70At5g06720ABRCN/A