Supplemental Table 5
Description
Locus information and gene names used in this study for shikimate pathway genes in Arabidopsis thaliana
Locus
Gene
Expression Oligo Subcellular
Designation in stems probe localizationa
Chorismate biosynthesis
3-deoxy-D-arabino-heptulosonate
7-phosphate synthase
At4g39980
At4g33510
DHS1
DHS2
up
+
chloroplast
chloroplast (?)
3-dehydroquinate synthase
At1g22410
At5g66120
DHS3
DQS
up
up
+
+
At3g06350
DHQD/SD
At2g21940
At4g39540
SK1
SK2
At3g26900
At2g35500
SK3
SK4
5-enolpyruvylshikimate-3phosphate synthase
At2g45300
At1g48860
EPSPS1
EPSPS2
chorismate synthase
Phe/Tyr biosynthesis
chorismate mutase
At1g48850
CS
At3g29200
3-dehydroquinate dehydratase /
shikimate dehydrogenase
shikimate kinase
prephenate aminotransferase
Tyr biosynthesis
arogenate dehydrogenase
Phe biosynthesis
arogenate dehydratase
P/A/L
Assignmentc
boxb
Reference
-
functional
homology
Keith et al. (1991)
Keith et al. (1991)
chloroplast
unclear
PAL
PAL
homology
homology
76% identity to DHS1 from Arabidopsis (Keith et al., 1991)
87% identical to DQS from tomato (Bischoff et al., 1996)
+
chloroplast
AL
homology
59% identical to DHQD/SD1 from tobacco (Bonner and Jensen, 1994)
up
up
+
+
other (?)
unclear
PL
PAL
homology
homology
53% identical to SK from tomato (Schmid et al., 1992)
53% identical to SK from tomato (Schmid et al., 1992)
down
up
+
+
chloroplast
chloroplast
-
homology
homology
31% identical to SK from tomato (Schmid et al., 1992)
17% identical to SK from tomato (Schmid et al., 1992)
-
-
chloroplast
chloroplast
PL
PL
functional
homology
Klee et al. (1987)
89% identical to EPSPS1 from Arabidopsis (Klee et al., 1987)
const.
+
chloroplast
-
homology
77% identical to CS from Corydalis (Schaller et al., 1991)
CM1
up
+
chloroplast
functional
(Eberhard et al., 1993; Mobley et al., 1999)
At5g10870
At1g69370
CM2
CM3
const.
const.
+
+
other
chloroplast
AL
-
functional
functional
(Eberhard et al., 1996; Mobley et al., 1999)
Mobley et al. (1999)
unknown
PNT
na
na
na
na
na
no gene cloned
const.
const.
+
+
chloroplast
chloroplast (?)
-
functional
functional
Rippert and Matringe (2002a)
Rippert and Matringe (2002b)
const.
At5g34930
At1g15710
tyrAAT1
tyrAAT2
At1g11790
ADT1d
down
+
mitochondria
-
structural
Hsieh and Goodman (2002)
At3g07630
At2g27820
ADT2d
ADT3
const.
up
+
+
chloroplast (?)
chloroplast (?)
-
structural
structural
Hsieh and Goodman (2002)
50% identical to PDT1 from Arabidopsis (Hsieh and Goodman, 2002)
At3g44720
ADT4
const.
+
other
-
structural
50% identical to PDT1 from Arabidopsis (Hsieh and Goodman, 2002)
At5g22630
ADT5
up
+
chloroplast
-
structural
48% identical to PDT1 from Arabidopsis (Hsieh and Goodman, 2002)
At1g08250
ADT6
up
+
chloroplast
-
structural
45% identical to PDT1 from Arabidopsis (Hsieh and Goodman, 2002)
At5g05730
ASA1
const.
+
chloroplast (?)
-
functional
Niyogi and Fink (1992)
At2g29690
At3g55870
ASA2
ASA3
const.
const.
+
+
chloroplast
other (?)
-
functional
homology
Niyogi and Fink (1992)
72% identical to ASA1 from Arabidopsis (Niyogi and Fink, 1992)
At1g25220
At1g24807
ASB1
ASB2
const.
const.
+
-
chloroplast
other
AL
-
functional
homology
Niyogi et al. (1993)
97% identical to ASB1 from Arabidopsis (Niyogi et al., 1993)
At1g24909
At1g25083
ASB3
ASB4
const.
const.
-
other
other
-
homology
homology
97% identical to ASB1 from Arabidopsis (Niyogi et al., 1993)
97% identical to ASB1 from Arabidopsis (Niyogi et al., 1993)
At1g25155
At5g57890
ASB5
ASB6
const.
const.
-
other
unclear
-
homology
homology
97% identical to ASB1 from Arabidopsis (Niyogi et al., 1993)
93% identical to ASB1 from Arabidopsis (Niyogi et al., 1993)
phosphoribosylanthranilate
transferase
At5g17990
At1g70570
PAT1
PAT2
const.
const.
+
+
chloroplast
chloroplast
PL
-
functional
homology
Rose et al., (1992)
14% identical to PAT1 from Arabidopsis (Rose et al., 1992)
phosphoribosylanthranilate
isomerase
At1g07780
At5g05590
PAI1
PAI2
const.
const.
+
-
chloroplast
chloroplast
PL
functional
functional
Li et al. (1995b)
Li et al. (1995b)
At1g29410
At2g04400
PAI3
IGPS1
const.
const.
+
+
chloroplast
unclear
PAL
functional
functional
Li et al. (1995b)
Li et al. (1995a)
tryptophan synthase alpha subunit
At5g48220
At3g54640
IGPS2
TSA1
const.
const.
+
+
chloroplast (?)
chloroplast
PL
homology
functional
63% identical to IGPS1 from Arabidopsis (Li et al., 1995a)
Radwanski et al., (1995)
tryptophan synthase beta subunit
At4g02610
At5g54810
TSA2
TSB1
const.
const.
+
+
other
chloroplast
PA
homology
functional
74% identical to TSA1 from Arabidopsis (Radwanski et al., 1995)
Last et al., (1991)
Trp biosynthesis
anthranilate synthase alpha subunit
anthranilate synthase beta subunit
indole-3-glycerol phosphate
synthase
const.
At4g27070
TSB2
+ chloroplast
homology
Last et al., (1991)
const.
At5g28237
TSB3
- unclear
AL homology
56% identical to TSB1 from Arabidopsis (Last et al., 1991)
a subcellular localization is based on targetP prediction (Emanuelsson et al., 2000), "other" denotes a subcellular localization other than chloroplast, mitochondrium, or secretory pathway, "(?)"
denotes a poor probability for the given localization (class 4 or class 5)
b Presence of P, A, and L promoter elements (Logemann et al., 1995) was determined using MotifMapper (Wanke et al., 2004), presence of motifs is indicated only if at least two of the three motifs
are present in the -1000 bp region of the corresponding genes
c "functional" denotes a biochemical and/or gentical proof, "homology" denotes that the annotation is based on sequence similarity to characterized plant genes only, "structural" denotes an
annotation based on domain structure and sequence similarity to bacterial and/or fungal genes only
d
designated PDT1 and PDT2 in Hsieh and Goodman (2002) as homologous to the yeast prephenate dehydratase
References for Supplemental Table 4
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