TABLE 3.
Type IV secretion system (T4SS) and type VI secretion systems (T6SS) are enriched in A. tumefaciens DRMs.
| Virulence-induction | |||||||||
| Name | Gene | UniprotID | Function | Membrane | DSM | DRM | ratio DRM/DSM [+vir] | p-value | |
| marker | HflC | atu2044 | A9CIC9 | Modulator of FtsH | ± | ± | ± | 8.23 | 0.002 |
| HflK | atu2045 | Q7CY01 | Modulator of FtsH | ± | ± | ± | 3.53 | 0.024 | |
| Atu3772 (QmcA) | atu3772 | A9CFM5 | Probable modulator of FtsH | ± | ± | ± | 2.83 | 0.003 | |
| FtsH | atu3710 | Q7CT50 | ATP-dependent zinc metalloprotease | ± | ± | ± | 2.92 | 0.002 | |
| vir (T4SS) | VirK | atu6156 | Q7CNV8 | VirA/G regulated protein | n.i. | n.i. | n.i. | – | – |
| VirA | atu6166 | P18540 | Two component chemoreceptor | + | ± | Only + vir | DRM only | 0.027 | |
| VirG | atu6178 | P07545 | Two component transcriptional activator | + | + | + | 3.07 | 0.017 | |
| VirB2 | atu6168 | P17792 | Pore/pilus like structure | Only + vir | n.i. | Only + vir | – | 0.423 | |
| VirB3 | atu6169 | P17793 | Pore/pilus like structure | Only + vir | n.i. | Only + vir | DRM only | 0.170 | |
| VirB4 | atu6170 | P17794 | Pore/pilus like structure | + | + | + | 5.37 | 0.000 | |
| VirB5 | atu6171 | P17795 | Pore/pilus like structure | Only + vir | Only + vir | Only + vir | DRM only | 0.271 | |
| VirB6 | atu6172 | P17796 | Pore/pilus like structure | n.i. | n.i. | Only + vir | – | 0.423 | |
| VirB7 | atu6173 | P17797 | Pore/pilus like structure | Only + vir | n.i. | + | DRM only | 0.038 | |
| VirB8 | atu6174 | P17798 | Pore/pilus like structure | + | Only + vir | Only + vir | 11.04 | 0.039 | |
| VirB9 | atu6175 | P17799 | Pore/pilus like structure | + | + | + | 9.70 | 0.009 | |
| VirB10 | atu6176 | P17800 | Pore/pilus like structure | + | + | + | 5.89 | 0.005 | |
| VirB11 | atu6177 | P07169 | Pore/pilus like structure | + | Only + vir | + | 15.77 | 0.079 | |
| VirC2 | atu6179 | P07166 | DNA binding | Only + vir | Only + vir | + | 30.44 | 0.004 | |
| VirC1 | atu6180 | P07165 | DNA binding | Only + vir | Only + vir | Only + vir | 2.48 | 0.076 | |
| VirD1 | atu6181 | P18591 | DNA binding, endonuclease | Only + vir | Only + vir | Only + vir | 1.39 | 0.297 | |
| VirD2 | atu6182 | P18592 | DNA binding, endonuclease | Only + vir | Only + vir | + | 1.78 | 0.165 | |
| VirD3 | atu6183 | P18593 | Unknown | + | + | + | 0.16 | 0.232 | |
| VirD4 | atu6184 | P18594 | Coupling factor | + | + | + | 7.69 | 0.068 | |
| VirD5 | atu6185 | A9CL19 | Secreted into plant cell | ± | n.i. | ± | – | 0.423 | |
| VirE1 | atu6189 | P08063 | Chaperone like protein for VirE2 | n.i. | n.i. | n.i. | – | – | |
| VirE2 | atu6190 | P08062 | DNA binding | + | + | + | 1.00 | 0.985 | |
| VirE3 | atu6188 | P08061 | Unknown | n.i. | n.i. | Only – vir | – | – | |
| VirF | atu6154 | Q7D2D9 | F-box protein | n.i. | n.i. | n.i. | – | – | |
| imp (T6SS) | TagE (ImpN) | atu4330 | Q7CUN1 | Serine/threonine protein kinase | + | ± | ± | DRM only | 0.037 |
| TagF (ImpM)* | atu4331 | Q7CUN2 | Serine/threonine phosphoprotein | ± | – | + | 4.50 | 0.010 | |
| TssM (ImpL) | atu4332 | A9CGF9 | IcmF family protein | ± | ± | ± | 3.39 | 0.029 | |
| TssL (ImpK) | atu4333 | Q7CUN4 | OmpA-like porin | ± | + | ± | 1.61 | 0.313 | |
| TssK (ImpJ) | atu4334 | A9CGG0 | Unknown | ± | ± | ± | 0.47 | 0.018 | |
| TagH (ImpI) | atu4335 | A9CGG1 | Putative fha-domain protein | ± | – | ± | 4.86 | 0.010 | |
| TssG (ImpH) | atu4336 | A9CGG2 | Unknown | + | n.i. | + | DRM only | 0.092 | |
| TssG (ImpG) | atu4337 | A9CGG3 | Unknown | + | + | + | 1.63 | 0.218 | |
| TssF (ImpF) | atu4338 | Q7CUN9 | Unknown | Only – vir | n.i. | ± | – | 0.423 | |
| TagJ (ImpE)* | atu4339 | Q7CUP0 | Unknown | + | – | + | DRM only | 0.021 | |
| TssC40 (ImpD) | atu4340 | A9CGG4 | Unknown | Only + vir | Only + vir | Only + vir | – | 0.730 | |
| TssC41 (ImpC) | atu4341 | A9CGG5 | Pore/pilus like structure | ± | + | + | 1.79 | 0.009 | |
| TssB (ImpB) | atu4342 | A9CGG6 | Pore/pilus like structure | + | + | + | 1.99 | 0.317 | |
| TssA (ImpA) | atu4343 | A9CGG7 | Unknown | ± | – | ± | 30.40 | 0.062 | |
| hcp (T6SS) | TssH (ClpV) | atu4344 | Q7CUP5 | ATP-dependent Clp protease | ± | – | ± | 7.13 | 0.013 |
| TssD (Hcp) | atu4345 | A9CGG8 | Hcp, needle complex | – | – | – | 14.44 | 0.067 | |
| Atu4346* | atu4346 | A9CGG9 | Unknown | n.i. | – | Only – vir | – | 0.423 | |
| Atu4347* | atu4347 | Q7CUP8 | Peptidoglycan amidase | ± | – | ± | 2.19 | 0.027 | |
| Tssl-1 (VgrG) | atu4348 | A9CGH0 | VgrG protein | ± | ± | ± | 1.68 | 0.019 | |
| Atu4349* | atu4349 | Q7CUQ0 | Unknown | ± | ± | + | 0.95 | 0.751 | |
| Atu4350* | atu4350 | A9CGH1 | Nuclease | + | ± | + | 1.18 | 0.490 | |
| Atu4351* | atu4351 | Q7CUQ2 | Unknown | ± | ± | + | 0.98 | 0.862 | |
| Atu4352* | atu4352 | A9CGH2 | Unknown | Only + vir | Only + vir | Only – vir | – | 0.423 | |
Stomatin/prohibitin/flotillin/HflKC proteins and FtsH do not respond to virulence-induction but are significantly enriched within DRMs. Proteins deduced from the vir operon are highly enriched in DRMs of virulence-induced cells. The T6SS consists of the imp and the hcp operon. Proteins encoded by the imp operon show a significant enrichment within the DRMs. For the hcp operon, only TssH, TssD and Atu4347 display a DRM enrichment. Proteins marked with an asterisk are dispensable for T6SS-dependent secretion according to Ma et al. (2014). Protein annotation according to UniProt database and Lin et al. (2013) and Ma et al. (2014). + or –: increased or decreased relative protein amount after virulence-induction; ±: no significant change in relative protein amount; n.i.: protein not identified; Only +/− vir: protein was only identified after/without virulence induction.