Table I.
Differentially up-regulated genes upon infection of Arabidopsis with R. fascians D188
| Gene | Function | Codea | Fold Change | ||
|---|---|---|---|---|---|
| 7 dpi | 14 dpi | 24 dpi | |||
| Cell organization and biogenesis | |||||
| At1g26770 | Expansin (putative; EXP10) | u14 | 1.45 | 3.39 | 4.76 |
| At1g31580 | Expressed protein | u101 | 2.89 | 0.86 | 0.95 |
| At1g48920 | Nucleolin (putative) | u82 | 0.95 | 1.32 | 2.13 |
| At1g69530 | Expansin (putative; EXP1) | u5 | 0.73 | 2.50 | 2.69 |
| At2g03090 | Expansin (putative; EXP15) | u92 | 0.81 | 1.69 | 4.22 |
| At2g43590 | Chitinase (putative) | u41 | 1.21 | 2.84 | 1.62 |
| At2g43610 | Glycoside hydrolase family 19 protein | u89 | 1.22 | 2.98 | 1.33 |
| At3g18000 | Phosphoethanolamine N-methyltransferase1 (PEAMT1) | 0.58 | 1.40 | 2.27 | |
| At3g18080 | Glycosyl hydrolase family 1 protein | u94 | 0.70 | 0.88 | 2.24 |
| At4g08950 | Phosphate-responsive protein (putative; EXO) | u54 | 1.49 | 0.62 | 2.29 |
| At4g28250 | β-Expansin (putative; EXPB3) | u11 | 0.60 | 1.86 | 4.30 |
| Development | |||||
| At3g17520 | Late embryogenesis abundant domain-containing protein | u102 | 0.99 | 0.94 | 2.76 |
| At3g51810 | Em-like protein GEA1 (EM1) | u99 | 1.03 | 1.05 | 3.61 |
| At5g03840 | Terminal flower 1 protein (TFL1) | u28 | 1.00 | 0.99 | 3.12 |
| At5g57390 | Ovule development protein (putative) | u36 | 1.23 | 1.46 | 2.01 |
| At5g28640 | SSXT protein-related/Gly-rich protein | u9 | 1.26 | 1.60 | 3.12 |
| Electron transport or energy pathway | |||||
| At1g66540 | Cytochrome P450 (putative) | u57 | 0.80 | 1.07 | 2.20 |
| At4g27080 | Thioredoxin family protein | u69 | 2.64 | 0.71 | 1.29 |
| At5g49730 | Ferric reductase-like transmembrane component family protein | u71 | 0.76 | 0.88 | 2.26 |
| Metabolism | |||||
| At1g06080 | Δ9 desaturase (ADS1) | u76 | 1.13 | 2.50 | 5.59 |
| At1g30820 | CTP synthase (putative)/UTP-ammonia ligase (putative) | u19 | 0.98 | 2.02 | 2.99 |
| At1g56430 | Nicotianamine synthase (putative) | u25 | 2.15 | 2.31 | 3.05 |
| At1g80050 | Adenine phosphoribosyltransferase 2 (APT2) | u77 | 1.57 | 2.06 | 4.44 |
| At1g78580 | Trehalose-6-phosphate synthase (putative) | u93 | 0.93 | 1.46 | 3.31 |
| At3g21420 | Oxidoreductase, 2OG-Fe(II) oxygenase family protein | u21 | 1.04 | 1.21 | 2.32 |
| At3g30775 | Pro oxidase, mitochondrial (POX; PRO1; ERD5) | u91 | 0.99 | 2.21 | 1.20 |
| At3g57010 | Strictosidine synthase family protein | u38 | 0.84 | 0.94 | 2.01 |
| At3g63440 | Cytokinin oxidase family protein | u105 | 0.99 | 1.48 | 2.26 |
| At4g02290 | Glycosyl hydrolase family 9 protein | u90 | 0.97 | 1.37 | 2.63 |
| At4g30140 | GDSL-motif lipase/hydrolase family protein | u87 | 1.45 | 2.93 | 2.06 |
| At4g30290 | Endoxyloglucan transferase (putative) | u40 | 1.65 | 2.48 | 5.88 |
| At5g13930 | Chalcone synthase/naringenin-chalcone synthase | u75 | 3.21 | 1.74 | 3.06 |
| At5g17220 | Glutathione S-transferase (putative) | u84 | 1.22 | 0.79 | 2.27 |
| At5g18670 | β-Amylase (putative; BMY3) | u81 | 0.56 | 1.11 | 2.16 |
| At5g45670 | GDSL-motif lipase/hydrolase family protein | u10 | 1.11 | 1.88 | 2.22 |
| At5g51210 | Gly-rich protein/oleosin | u50 | 1.12 | 0.97 | 2.39 |
| At5g55250 | S-adenosylmethionine:carboxyl methyltransferase family protein | u49 | 1.09 | 1.49 | 2.54 |
| Protein metabolism | |||||
| At2g47020 | Peptide chain release factor (putative) | u27 | 3.24 | 0.99 | 1.61 |
| At4g25740 | 40S ribosomal protein S10 (RPS10A) | u51 | 1.30 | 1.25 | 2.01 |
| At5g19110 | Extracellular dermal glycoprotein (EDGP)-related | u16 | 1.45 | 2.21 | 1.23 |
| At5g53450 | Protein kinase family protein | u60 | 3.61 | 4.52 | 6.27 |
| Response to biotic or abiotic stimulus | |||||
| At1g23130 | Bet v I allergen family protein | u100 | 2.42 | 0.67 | 0.20 |
| At1g56150 | Auxin-responsive family protein | u26 | 2.22 | 1.52 | 0.61 |
| At1g73260 | Trypsin and protease inhibitor/Kunitz family protein | u45 | 2.05 | 1.12 | 0.65 |
| At1g73330 | Protease inhibitor (putative; DR4) | u61 | 2.06 | 0.65 | 0.13 |
| At2g38310 | Expressed protein | u52 | 2.31 | 1.00 | 1.04 |
| At2g38870 | Protease inhibitor (putative) | u35 | 2.62 | 1.61 | 0.50 |
| At2g43510 | Trypsin inhibitor (putative) | u53 | 2.12 | 1.46 | 0.67 |
| At2g43530 | Trypsin inhibitor (putative) | u56 | 2.20 | 0.60 | 0.45 |
| At3g57240 | β-1,3-Glucanase (BG3) | u29 | 1.07 | 2.17 | 1.73 |
| At4g30660 | Low-temperature and salt-responsive protein (putative) | u79 | 2.15 | 0.84 | 1.12 |
| RNA/DNA metabolism | |||||
| At1g02840 | Pre-mRNA splicing factor SF2 (SF2)/SR1 protein | u66 | 1.06 | 1.03 | 2.01 |
| At3g27060 | Ribonucleotide reductase (putative) | u42 | 1.45 | 2.08 | 2.21 |
| Signal transduction | |||||
| At1g10470 | Two-component-response regulator (ARR4) | u73 | 1.09 | 2.20 | 3.20 |
| At1g19050 | Two-component-response regulator (ARR7) | u1 | 1.81 | 3.75 | 8.88 |
| At2g40670 | Two-component-response regulator (ARR16) | u13 | 1.04 | 1.38 | 2.01 |
| At2g41310 | Two-component-response regulator (ARR8) | u8 | 1.01 | 1.37 | 2.24 |
| At2g46070 | Mitogen-activated protein kinase MAPK (putative; MPK12) | u86 | 0.96 | 1.00 | 2.31 |
| At3g57040 | Two-component-response regulator (ARR9) | u15 | 0.98 | 1.26 | 3.06 |
| At5g15230 | Gibberellin-regulated protein 4 (GASA4)/GA-responsive protein 4 | u39 | 1.68 | 2.37 | 2.49 |
| At5g62920 | Two-component-response regulator (ARR6) | u104 | 1.65 | 2.80 | 6.57 |
| Transcription factor | |||||
| At1g04250 | Auxin-responsive protein/IAA-induced protein 17 (IAA17) | u55 | 1.37 | 1.58 | 2.26 |
| At1g56170 | Transcription factor (putative) | u78 | 1.51 | 1.07 | 2.01 |
| At1g67260 | Pseudogene (putative) cycloidea cyc4 protein | 1.00 | 1.48 | 2.50 | |
| At1g68360 | Zinc finger protein-related | u17 | 1.13 | 1.43 | 2.65 |
| At1g71030 | Myb family transcription factor | u23 | 0.56 | 0.73 | 2.35 |
| At2g28510 | Dof-type zinc finger domain-containing protein | u80 | 0.79 | 1.73 | 2.86 |
| At3g15540 | Auxin-responsive protein/IAA-induced protein 19 (IAA19) | u48 | 1.32 | 1.49 | 2.72 |
| At3g16770 | AP2 domain-containing protein RAP2.3 (RAP2.3) | u74 | 0.85 | 1.06 | 2.15 |
| At3g25710 | Basic helix-loop-helix (bHLH) family protein | u62 | 0.97 | 1.27 | 2.27 |
| At4g37750 | Ovule development protein aintegumenta (ANT) | u63 | 1.14 | 1.54 | 2.97 |
| At5g25190 | Ethylene-responsive element-binding protein (putative) | u58 | 1.28 | 2.15 | 4.11 |
| At5g47370 | Homeobox-Leu zipper protein 2 (HAT2)/HD-ZIP protein 2 | u7 | 1.55 | 1.59 | 3.15 |
| At5g50010 | Expressed protein/similar to SAC51 transcription factor | u10 | 0.99 | 1.33 | 2.32 |
| Transport | |||||
| At1g19450 | Integral membrane protein (putative)/sugar transporter family protein | u103 | 0.99 | 1.49 | 2.09 |
| At1g59740 | Proton-dependent oligopeptide transport (POT) family protein | u24 | 1.29 | 1.51 | 3.09 |
| At2g45180 | Protease inhibitor/seed storage/lipid transfer protein (LTP) | u97 | 2.20 | 0.95 | 0.38 |
| At3g25620 | ABC transporter family protein | 0.97 | 1.03 | 3.30 | |
| At3g25620 | ABC transporter family protein | u46 | 0.86 | 0.88 | 5.88 |
| At4g22520 | Protease inhibitor/seed storage/lipid transfer protein (LTP) | 3.10 | 4.91 | 3.10 | |
| At4g27780 | Acyl-CoA binding protein 2 (ACBP2) | u109 | 1.03 | 1.11 | 2.02 |
| At5g13740 | Sugar transporter family protein | u83 | 1.51 | 1.67 | 2.41 |
| At5g50200 | Wound-responsive gene | u20 | 1.30 | 2.84 | 1.18 |
| Others | |||||
| At1g02205 | CER1 protein | 1.08 | 1.06 | 2.33 | |
| At1g03870 | Fasciclin-like arabinogalactan protein (FLA9) | u106 | 2.91 | 0.78 | 0.63 |
| At1g48310 | SNF2 domain-containing protein/helicase domain protein | u67 | 1.18 | 0.95 | 2.39 |
| At1g66100 | Thionin (putative) | u4 | 1.60 | 0.92 | 2.62 |
| At1g70560 | Alliinase C-terminal domain-containing protein | u33 | 1.17 | 1.90 | 2.60 |
| At2g34700 | Pollen Ole e 1 allergen and extensin family protein | u64 | 3.02 | 7.24 | 7.94 |
| At3g09390 | Metallothionein protein (putative; MT2A) | u22 | 2.24 | 0.79 | 1.01 |
| At3g13520 | Arabinogalactan protein (AGP12) | u31 | 2.47 | 0.82 | 0.89 |
| At3g16640 | Translationally controlled tumor family protein | u68 | 0.98 | 0.94 | 2.08 |
| At4g04810 | SeIR domain-containing protein | 2.40 | 0.62 | 0.38 | |
| At4g04830 | SeIR domain-containing protein | u111 | 2.94 | 0.65 | 0.30 |
| At4g24780 | Pectate lyase family protein | u85 | 0.71 | 1.24 | 2.10 |
| At4g31290 | ChaC-like family protein | u70 | 1.43 | 1.28 | 2.92 |
| At5g48850 | Male sterility MS5 family protein | u72 | 2.58 | 0.94 | 0.62 |
| Unknown | |||||
| At1g15270 | Expressed protein | u59 | 2.09 | 1.05 | 1.12 |
| At1g29980 | Expressed protein | u34 | 1.15 | 1.65 | 2.16 |
| At1g64980 | Expressed protein | u88 | 1.39 | 2.27 | 2.42 |
| At1g68250 | Expressed protein | u43 | 0.90 | 0.87 | 2.71 |
| At2g27385 | Expressed protein | 1.24 | 1.11 | 2.12 | |
| At2g30760 | Hypothetical protein | u44 | 1.28 | 1.50 | 3.03 |
| At2g32280 | Expressed protein | u18 | 1.27 | 1.56 | 2.03 |
| At2g32560 | F-box family protein | 1.18 | 1.26 | 2.49 | |
| At2g34160 | Expressed protein | u47 | 2.06 | 1.19 | 1.04 |
| At2g39870 | Expressed protein | u12 | 0.96 | 1.11 | 2.32 |
| At3g05730 | Expressed protein | u96 | 1.26 | 2.25 | 1.89 |
| At3g08030 | Expressed protein | u30 | 0.93 | 1.36 | 2.73 |
| At3g11720 | Expressed protein | 1.00 | 1.39 | 2.14 | |
| At3g16660 | Expressed protein | u110 | 1.10 | 2.63 | 1.67 |
| At3g19200 | Hypothetical protein | u107 | 1.10 | 1.54 | 3.59 |
| At3g56360 | Expressed protein | u65 | 1.07 | 1.25 | 2.85 |
| At4g09840 | Expressed protein | u95 | 1.07 | 0.97 | 2.07 |
| At4g30410 | Expressed protein | u2 | 1.20 | 1.58 | 2.94 |
| At5g03545 | Expressed protein | u37 | 3.21 | 1.07 | 0.25 |
| At5g05250 | Expressed protein | u32 | 1.32 | 1.72 | 2.78 |
| At5g19260 | Expressed protein | u3 | 1.21 | 1.76 | 3.98 |
| At5g24660 | Expressed protein | u98 | 3.40 | 1.14 | 0.63 |
| At5g52900 | Expressed protein | u6 | 1.17 | 1.64 | 3.22 |
a
Refers to genes in the left panel of Figure 4.