Figure S1. Schematic diagram of vector pU1391W used to study subcellular localization of proteins. RB and LB, right and left T-DNA border;; Hpt, hygromycin phosphotransferase gene; GFP, green fluorescent protein gene; PWRKY13, rice OsWRKY13 promoter; NOS, napoline synthase polyadenylation signal.

RB PWRKY13 target gene GFP NOS Hpt LB

HindIII PstI BamHI EcoRI

Figure S2. Gel mobility shift assays. The electrophoresis was performed with the gel plates of 6 cm in length, which could not clearly distinguish different sizes of DNA-protein complexes.

The nuclear proteins were from 8 h after mock-inoculated (control) or JL691-inoculated Mudanjiang 8. DNA probes are 39- to 51-bp in length (Supplemental Table 2).

(a) D

53I8

D53

I10

D53

I12

D53

I14

D53

I16

D53

I18

D53

I20

D53

I22

D53

I24

Mock inoculation

D53

I8D

53I1

0

D53

I12

D53

I14

D53

I16

D53

I18

D53

I20

D53

I22

D53

I24

Pathogen (JL691) inoculation

D53

I12-

1 (p

ath

ogen

inoc

ula

tion

)

D53

I12-

2 (p

ath

ogen

inoc

ula

tion

)

D53

I16-

1 (p

ath

ogen

inoc

ula

tion

)

D53

I16-

2 (p

ath

ogen

inoc

ula

tion

)

To determine the pathogen-responsive DNA-protein binding regions in probes D53I12 and D53I16 as shown in Supplemental Fig. 2a, four 17- to 25-bp probes (Supplemental Table 2) from the two long probes were examined for their binding ability to nuclear proteins from pathogen-inoculated rice cultivar Mudanjiang 8. The gel mobility shift assay shows that D53I8-1, D53I12-1 do not contain protein-binding site and D53I12-2, D53I16-1 and D53I16-2 contain protein-binding sites.

(b)

To further define the pathogen-responsive DNA-protein binding regions in probes D53I12-2 and D54I16-2 as shown in Supplemental Fig. 2b, four 9- to 13-bp probes (Supplementary Table 2) from the two long probes were examined for their binding ability to nuclear proteins from pathogen-inoculated rice cultivar Mudanjiang 8. The gel mobility shift assay shows that D53I12-2-1, D53I12-2-2 and D53I16-2-2 contain protein-binding sites and D53I16-2-1 do not contain protein-binding site.

D53

I12-

2-1

(pat

hog

en in

ocu

lati

on)

D53

I12-

2-2

(pat

hog

en in

ocu

lati

on)

D53

I16-

2-1

(pat

hog

en in

ocu

lati

on)

D53

I16-

2-2

(pat

hog

en in

ocu

lati

on)

(c)

To further define the pathogen-responsive DNA-protein binding regions in probes D53I12-2-1and D53I16-2-2 as shown in Supplemental Fig. 2c, six 5- to 7-bp probes (Supplementary Table 2) from the two long probes were examined for their binding ability to nuclear proteins from pathogen-inoculated rice cultivar Mudanjiang 8. The gel mobility shift assays show that all the probes contain protein-binding sites, indicating that the protein-binding sites in the two probes shown in Supplemental Fig. 1C can not be further defined.

(d)

D53

I12-

2-1-

1 (p

ath

ogen

inoc

ula

tion

)

D53

I12-

2-1-

2 (p

ath

ogen

inoc

ula

tion

)

D53

I12-

2-1-

3 (p

ath

ogen

inoc

ula

tion

)

D53

I16-

2-2-

1 (p

ath

ogen

inoc

ula

tion

)

D53

I16-

2-2-

2 (p

ath

ogen

inoc

ula

tion

)

D53

I16-

2-2-

3 (p

ath

ogen

inoc

ula

tion

)

(e)

D53

I16-

2-2

(M)

D53

I12-

2-1

(P)

D53

I16-

2-2

(P)

D53

I12-

2-1

(M)

The nuclear proteins were from 8 h after mock-inoculated (M, control) or pathogen (JL691)-inoculated (P) Mudanjiang 8. The gel mobility shift assay shows that D53I12-2-1 and D53I16-2-2 contain protein-binding sites, which have the same protein binding patterns as D53I12 and D54I16 shown in Supplemental Fig. 2a.