Table 1. Selected sX13-regulated genes validated by qRT-PCR analysis.
| Locusa | Annotated gene productb | 4G-motifc | Microarray – Fold-change (ΔsX13/wt)d | qRT-PCR – Fold-change (ΔsX13/wt)e | ||
| NYG | MMA | NYG | MMA | |||
| Upregulated genes (Δ sX13 /wt) | ||||||
| XCV0678 | AlgR; two-component system regulatory protein | a,a,a | 1.8 | — | 2.5±0.23 | n.t. |
| XCV1768 | Hfq; host factor-I protein | b | 1.6 | — | 2.4±0.08 | 1.6±0.31 |
| XCV2186 | methyl-accepting chemotaxis protein | a | 7.7 | — | 2.1±0.34 | 10.2±4.63 |
| XCV2814 | PilE; type IV pilus pilin | — | 2.8 | — | 3.3±0.36 | n.t. |
| XCV2819 | type IV pilus assembly protein PilW | a | 3.7 | 4.0 | 3.4±0.37 | 5.5±3.0 |
| XCV2821 | type IV pilus assembly protein FimT | a | 4.3 | 7.4 | 4.2±0.32 | 3.4±1.27 |
| XCV3067 | PilU; type IV pilus assembly protein ATPase | a | 1.8 | — | 1.7±0.29 | n.t. |
| XCV3096 | ComEA-related DNA uptake protein | — | — | 4.2 | n.t. | 1.9±0.12 |
| XCV3233 | PilG; type IV pilus response regulator | a,b | — | 2.0 | 2.3±0.26 | 4.1±1.71 |
| XCV3500 | PilN; type IV pilus assembly protein | — | 2.7 | — | 2.7±0.16 | n.t. |
| XCV3927 | putative secreted protein | a | — | 1.7 | 5.6±0.45 | 8.3±4.54 |
| Downregulated genes (Δ sX13 /wt) | ||||||
| XCV1315 | HrpX; AraC-type transcriptional regulator | — | 0.6 | — | 0.6±0.01 | 0.7±0.13 |
| XCV1957 | CheY; chemotaxis response regulator | — | 0.4 | — | 0.1±0.04 | n.t. |
| XCV2022 | FliC; flagellin and related hook-associated proteins | — | 0.2 | — | 0.06±0.03 | 1.0±0.39 |
| XCV3572 | TonB-dependent outer membrane receptor | a | 0.2 | — | 0.2±0.04 | 0.9±0.24 |
| Additional genes tested by qRT-PCR | ||||||
| XCV0173 | putative secreted protein | a,b,b,b | — | — | 1.9±0.19 | 0.8±0.26 |
| XCV0612 | ATPase of the AAA+ class | a | — | — | 1.0±0.06 | 0.8±0.26 |
| XCV1533 | AsnB2; asparagine synthase | b | — | — | 1.0±0.04 | 1.0±0.17 |
| XCV3232 | PilH; type IV pilus response regulator | a | — | — | 2.2±0.07 | 1.9±0.67 |
| XCV3573 | putative transcriptional regulator, AraC family | a | — | — | 0.2±0.11 | n.t. |
| XCV0324 | type III effector protein XopS | — | — | — | 0.6±0.05 | n.t. |
a
, bold letters indicate genes with known TSS [16].
b
, refers to Thieme et al. (2005) [32].
c
, presence of a 4G-motif within the 5′-UTR or 100 bp upstream of translation start codon if TSS is unknown (a) and within 100 bp downstream of start codon (b) (see Figure S4).
d
, genes not detected as expressed are marked with —.
e
, values represent mean fold-change and standard deviation (see Figure 4);
n.t. - not tested.