Table III.

Arabidopsis genes differentially regulated during the early interaction with G. cichoracearum

LS, Light-sensitive genes according to Smith et al. (2004). Bold type indicates genes that are induced or repressed by the large majority of other biotic stresses (e.g. bacterial pathogens, nonhost bacteria, and bacterial and fungal elicitors including LPS and flg22, fungal necrotrophs and biotrophs, according to data obtained from www.bbc.botany.u-toronto.ca). Underlined type indicates genes that appear to be specifically induced or repressed by G. cichoracearum or G. orontii.

AGI No.	EST No.	Gene Producta	Subcellular Localizationb	Functional Categoryb	Fold Changec
Induced
At4g33120	F1A4T7	Cyclopropane-fatty-acyl-phospholipid synthase-like protein	Cytosol	Metabolism	2.37
At2g30140LS	189L18T7	UDP-glucoronosyl and UDP-glucosyl transferase family protein. UGT87A1/A2	Endomembranes	Metabolism	1.90
At4g22720	186N2T7	Glycoprotease M22 family protein, similar to sialylglycoprotease	Endomembranes	Metabolism	2.33
At3g02870	241A20T7	Inositol-1(or 4)-monophosphatase 3, (IMP3) putative	Endomembranes	Metabolism	2.49
At3g16520LS	119P15T7	UDP-glucoronosyl/UDP-glucosyl transferase family protein. UGT88A1	Endomembranes	Metabolism	1.97
At4g29950LS	H10A12T7	Microtubule-associated protein	Mitochondrion	Metabolism	2.39
At2g34500	122P6XP	Cytochrome P450 family protein, C-22 sterol desaturase CYP710A1	Mitochondrion	Metabolism	2.69
At1g73480LS	179H9XP	Hydrolase, α/β-fold family protein	Chloroplast	Metabolism	2.09
At4g28680	193C4T7	Tyr decarboxylase, putative	Cytosol	Metabolism	3.11
At5g40760	184F4T7	Glc-6-P 1-dehydrogenase/G6PD (ACG9)	Cytosol	Metabolism	2.16
At5g67030LS	133D24T7	Zeaxanthin epoxidase (ZEP; ABA1)	Chloroplast	Metabolism	3.24
At1g18460LS	G2G11T7	Lipase family protein	Cytosol	Metabolism	2.22
At2g05070	118I1T7 119A21T7 92F2T7	Chlorophyll a/b-binding protein/LHCII type II (LHCB2.2)	Chloroplast	Energy	8.95
At1g44446LS	103D24XP	Chlorophyll a oxygenase (CAO)	Chloroplast	Energy	6.80
At3g08940LS	45E2T7	Chlorophyll a/b-binding protein (LHCB4.2; CP29)	Chloroplast	Energy	4.09
At1g70290 At1g23880	CI0021	Trehalose-6-P synthase, putative, similar to trehalose-P synthase/trehalose 6P phosphatase (TPS6 and TPS8)	Endomembranes	Energy	5.63
At2g34430	110O24T7	Chlorophyll a/b-binding protein/LHCII type I (LHB1B1)	Chloroplast	Energy	3.53
At5g45820LS	92F7T7	CBL-interacting protein kinase 20 (CIPK20)	Cytosol	Signal transduction	3.91
At2g42590	153H8T7	14-3-3 protein GF14 (GRF9)	Chloroplast/nucleus	Signal transduction	1.49
At3g17510LS	192B23T7	CBL-interacting protein kinase 1 (CIPK1)	Cytosol	Signal transduction	2.19
At1g04530LS	E1H4T7	Expressed protein, with HAT motif	Unknown	RNA processing	3.64
At3g53420LS	134N2T7	Plasma membrane intrinsic protein 2A (PIP2A)/aquaporin PIP2.1	Plasma membrane	Cellular transport	2.11
At3g52400	86D5T7	Syntaxin protein of plants SYP122	Plasma membrane	Cellular transport	2.92
At5g25520	K2B12T7	PHD finger protein related, transcription elongation factor-related	Nucleus	Transcription	2.67
At3g59060LS	224K3T7	Basic helix-loop-helix (bHLH) family protein	Nucleus	Transcription	1.94
At4g11970	179L10T7	YT521-B-like family protein, RNA splicing-related protein	Cytosol	Transcription	2.66
At2g25080LS	121P8T7	Phospholipid hydroperoxide glutathione peroxidase, PHGPx (GPX1)	Chloroplast	Defense	2.16
At3g56940LS	202D1T7	Putative ZIP protein (AT103)	Chloroplast	Defense	3.83
At5g44580	96O24T7	Expressed protein	Endomembranes	Unknown	2.64
At3g54500LS	158J22T7	Expressed protein	Unknown	Unknown	2.66
At1g54390	192A3T7	PHD finger protein-related	Intracellular /unknown	RNA processing	2.12
At1g11200	122I2XP	Expressed protein	Endomembranes	Unknown	2.39
At4g01880	124K8T7	Expressed protein	Chloroplast	Unknown	2.54
At4g21850	G3C11T7	Met sulfoxide reductase domain-containing protein/SeIR	Unknown	Unknown	2.24
At2g30520LS	G8G6T7	Signal transducer of phototropic response (RPT2)	Nucleus	Unknown	3.65
At5g19190	186F13T7	Expressed protein	Unknown	Unknown	2.17
Repressed
At5g23660LS	42B2T7	Nodulin MtN3 family protein	Endomembranes	Metabolism	−2.21
At2g33830LS (two sequences)	K4F7TP	Dormancy/auxin-associated family protein	Cytosol/nucleus	Metabolism	−2.83
At2g25610	174O23T7	H+-transporting two-sector ATPase, C-subunit family protein	Vacuole membrane	Metabolism	−1.84
At5g26570LS	151D20XP	Similar to starch excess protein (SEX1) chloroplastidic phosphoglucan water dikinase (PWD)	Chloroplast	Metabolism	−5.99
At1g27630	G8D10T7	Cyclin family protein	Nucleus	Metabolism	−3.27
At3g10410LS	114J9T7	Ser carboxypeptidase III, putative	Endomembranes	Metabolism	−2.18
At2g36390LS	82F10T7	1,4-α-glucan branching enzyme/starch branching enzyme class II (SBE2-1)	Chloroplast	Metabolism	−1.91
At2g29630LS	173E13T7	Thiamine biosynthesis family protein/thiC	Chloroplast	Metabolism	−4.03
At1g18170	113C9XP	Immunophilin/FKBP-type peptidyl-prolyl cis-trans-isomerase family protein (PPiase; rotamase)	Chloroplast	Metabolism	−1.91
At3g19960	H3A1T7	Myosin (ATM)	Phragmoplast	Metabolism	−2.28
At1g79440LS	93P2T7	Mitochondrial succinic semialdehyde dehydrogenase (ALDH5F1)	Mitochondrial Matrix	Metabolism	−2.45
At2g28900LS	88L10XP	Similar to mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein	Mitochondrial inner membrane	Signal transduction	−3.66
At3g59350LS	172P5T7 H3D6T7	Ser/Thr protein kinase, putative, similar to Pto kinase interactor 1 (Pti1)	Cytosol	Signal transduction	−5.09
At4g32551	192K6T7	WD-40 repeat family protein, similar to LEUNIG; β-transducin-like protein	Nucleus	Signal transduction	−3.27
At3g24450	E11B5T7	Copper-binding family protein	Endomembranes	Signal transduction	−14.36
At4g25160LS	173N1T7	Protein kinase family protein	Chloroplast/cytosol	Signal transduction	−3.19
At5g61380LS	H1G8T7	ABI3-interacting protein 1 (AIP1), iden tical to pseudoresponse regulator 1	Nucleus	Signal transduction	−12.2
At1g56300LS	E6H4T7	DNAJ heat shock N-terminal domain-containing protein	Mitochondrion	Cellular transport	−2.13
At5g63780LS	F4B7T7	Zinc finger (C3HC4-type RING finger) family protein	Chloroplast/nucleus	Transcription	−2.93
At3g53460LS	91L18T7	Ribonucleoprotein (29-kD), chloroplast/RNA-binding protein cp 29	Chloroplast	Transcription	−3.07
At1g12760	187A11T7	Similar to zinc finger (C3HC4-type RING finger) family protein, RING finger protein 12	Chloroplast/nucleus	Transcription	−3.45
At1g78630	149D9T7	Ribosomal protein L13 family protein	Chloroplast	Transcription	−2.31
At3g07650LS	151B13XP	CONSTANS gene family	Nucleus	Transcription	−2.15
At5g20630LS	E8E6T7	Germin-like protein (GER3)	Extracellular matrix	Defense	−6.05
At4g30660LS	231P23T7	Low-temperature and salt-responsive protein, putative, similar to LTI6A	Endomembranes	Defense	−2.08
At1g06460LS	186C19T7	Small heat shock family protein/hsp20 (31.2 kD) family protein	Mitochondrion	Defense	−2.45
At5g05740	115N4T7	S2P-like putative metalloprotease, homolog of EGY1	Chloroplast	Unknown	−1.98
At4g26670LS	143E9T7	Mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family protein, weak similarity to subunit TIM17 A	Mitochondrion	Unknown	−4.19
At3g47860LS	103E18T7	Expressed protein	Chloroplast	Unknown	−4.31
At2g40080LS	118E14T7	ELF4-like protein	Unknown	Unknown	−12.03
At5g14920LS	193O8T7	GA-regulated protein 1 precursor	Endomembranes	Unknown	−2.83
At2g36320	E11A4T7	Expressed protein, zinc finger (AN1-like) family protein	Nucleus	Unknown	−5.64
At3g63160LS	206G8T7	Expressed protein	Chloroplast	Unknown	−6.89

^aGenes showing the same trend of induction or repression among the three tested genotypes (Col-0, npr-1, and jar-1).

^bSubcellular localizations and functional categories were extracted from the TAIR Web site (www.arabidopsis.org).

^cAverage of the fold change between uninfected (0 hpi) and 18 hpi samples of the three genotypes.