In initial experiments we compared the gene expression profiles in leaf tissues inoculated with DC3000, the hrpS regulatory mutant (1), or the hrcC secretory mutant (1). Comparison of gene expression profiles using DC3000 and the hrpS mutant enabled us to identify 385 genes that are differentially regulated at >2-fold (a ratio <0.5 for repressed genes or >2.0 for induced genes in at least two of the three biological replicates; R.T., E. Bray-Speth, and S.Y.H., unpublished results). A similar profile was obtained using DC3000 and the hrcC mutant. Surprisingly, we found many jasmonic acid (JA)-response genes among DC3000-regulated genes. The TTSS was recently found to influence the production of the phytotoxin coronatine (COR), a molecular mimic of JA, in DC3000 (2, 3). Further analysis using the DC3118 COR^– mutant (ref. 4; defective in the production of COR) led to identification of a large number of COR-responsive genes. In order to identify TTSS-regulated host genes, we compared leaf tissues inoculated with the COR^- mutant (defective in only COR production) to that of tissues inoculated with the COR^- hrpS double mutant (defective in both COR production and type III secretion). Using this comparison, we selected genes that were differentially expressed at >2.0-fold in two biological replicates of experiment I and at >1.8-fold in both biological replicates of experiment II. That analysis identified the 117 genes contained in Table 2. The differential expression patterns in experiments I and II are globally similar. The quantitative difference between experiments I and II may suggest an additive contribution of COR toxin to the regulation of at least some of these host genes. To examine the reproducibility of our microarray results, we also conducted RNA blot analysis of 10 selected genes (At2g38540, At1g72610, At1g12090, At2g10940, At1g03870, At1g29670, At3g16240, At2g17500, At5g26340, and At4g02380), all independently confirming their TTSS-dependent expression (R.T., E. Bray-Speth, and S.Y.H., unpublished results).

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