TABLE 2.
Channels, β-porins, and pore-forming toxinsa
| Family and transporterb | TC no. | ORF | No. of TMSs | Putative substrate | Occurrence | Comments | E value | PRSS P value | Xylella annotation | COG |
|---|---|---|---|---|---|---|---|---|---|---|
| Channels | ||||||||||
| VIC | 1.A.1.2.3 | XF1426 | 6 | Cation | BAE | Voltage-sensitive K+ channel | 1e-21 | 4.9873e-23 | Ion transporter | COG1226 (79 proteins), Kef-type K+ transport systems, predicted NAD-binding component |
| MIP | 1.A.8.1.1 | XF2267 | 5 | Small molecule | BAE | Glycerol facilitator | 5e-46 | 5.8223e-29 | Glycerol uptake facilitator protein | COG0580 (36 proteins), glycerol uptake facilitator and related permeases (major intrinsic protein family) |
| MscL | 1.A.22.1.1 | XF0039 | 2 | Protein or ion | B | Large mechanosensitive ion channel | 8e-35 | 8.7563e-28 | Large-conductance mechanosensitive channel | COG1970 (19 proteins), large-conductance mechanosensitive channel |
| MscS | 1.A.23.1.2 | XF0437 | 5 | Ions | BAE | Major MscS mechanosensitive ion channel | 3e-04 | 2.7709e-06 | Conserved hypothetical protein | COG0668 (80 proteins), small-conductance mechanosensitive channel |
| MscS | 1.A.23.1.2 | XF1258 | 4 | Ions | BAE | Major MscS mechanosensitive ion channel | 2e-47 | 3.2616e-30 | Small-conductance mechanosensitive ion channel | COG0668 (80 proteins), small-conductance mechanosensitive channel |
| β-Porins | ||||||||||
| POP | 1.B.5.1.2 | XF0321 | 0 | Pyrophosphate | B− | Pyrophosphate-selective porin | 7e-17 | 3.0706e-14 | Porin O precursor | No COG |
| POP | 1.B.5.1.2 | XF0975 | 0 | Pyrophosphate | B− | Pyrophosphate-selective porin | 4e-13 | 8.3331e-14 | Polyphosphate-selective porin O | No COG |
| OOP | 1.B.6.1.2 | XF0343 | 1? | B− | OmpF porin | 2e-38 | 5.6084e-35 | Outer membrane protein | COG2885 (60 proteins), outer membrane protein and related peptidoglycan-associated (lipo) proteins | |
| FadL | 1.B.9.1.1 | XF1053 | 0 | Hydrophobic | B− | Fatty acid outer membrane porin | 1e-33 | 1.0349e-23 | Outer membrane protein | COG2067 (19 proteins), long-chain fatty acid transport protein |
| FUP | 1.B.11.3.1 | XF0081 | 1 | Fimbrial structure | B− | Fimbrial usher | e-119 | 4.2124e-47 | Outer membrane usher protein precursor | COG3188 (31 proteins), PapC-like porin protein involved in fimbrial biogenesis |
| AT | 1.B.12.5.1 | XF0267 | 1 | Virulence factor | B− | Autoexporter of serine protease | 7e-51 | 1.5727e-24 | Serine protease | 2 domains: 1, XF0267_1, COG1404 (68 proteins), subtilisin-like serine proteases: 2, XF0267_2, no COG |
| AT | 1.B.12.5.1 | XF1026 | 1 | Virulence factor | B− | Autoexporter of serine protease | 8e-48 | 1.2144e-23 | Serine protease | 2 domains: 1, XF1026_1, COG1404 (68 proteins), subtilisin-like serine proteases: 2, XF1026_2, no COG |
| AT | 1.B.12.5.1 | XF1851 | 0 | Virulence factor | B− | Autoexporter of serine protease | 1e-51 | 1.3276e-26 | Serine protease | 2 domains: 1, XF1851_1, no COG: 2, XF1851_2, COG1404 (68 proteins), subtilisin-like serine proteases |
| OMR | 1.B.14.1.1 | XF2134 | 0 | Iron siderophore | B− | FepA ferric enterobactin receptor | 1e-23 | 3.3329e-20 | Ferric enterobactin receptor | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMR | 1.B.14.1.1 | XF2137 | 0 | Iron siderophore | B− | FepA ferric enterobactin receptor | 8e-19 | 2.4582e-15 | Ferric enterobactin receptor | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMR | 1.B.14.1.4 | XF0599 | 0 | Iron hydroxamate | B− | FhuA ferrichrome receptor | 1e-35 | 2.5692e-26 | TonB-dependent receptor for iron transport | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMR | 1.B.14.2.3 | XF0384 | 0 | Iron siderophore | B− | HemR heme (hemin) receptor | 2e-09 | 8.9988e-11 | Outer membrane hemin receptor | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMR | 1.B.14.2.3 | XF1496 | 0 | Iron siderophore | B− | HemR heme (hemin) receptor; Blast with filter E value, 6e-04 | 7e-05 | 4.4425e-08 | TonB-dependent receptor for iron transport | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMR | 1.B.14.3.1 | XF0339 | 0 | Vitamin B12 | B− | BtuB cobalamin receptor | 2e-19 | 2.3654e-10 | Conserved hypothetical protein | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMR | 1.B.14.3.1 | XF0550 | 0 | Vitamin B12 | B− | BtuB cobalamin receptor | 1e-15 | 1.3333e-11 | Conserved hypothetical protein | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMR | 1.B.14.3.1 | XF2237 | 0 | Vitamin B12 | B− | BtuB cobalamin receptor | 4e-16 | 8.6932e-10 | Conserved hypothetical protein | COG1629 (205 proteins), outer membrane receptor proteins, mostly Fe transport |
| OMF | 1.B.17.1.1 | XF2586 | 1 | Hemolysin, drugs, etc. | B− | TolC outer membrane exporter | 4e-62 | 2.5737e-31 | Outer membrane export factor | COG1538 (64 proteins), outer membrane protein |
| OMA | 1.B.18.3.1 | XF2370 | 0 | EPS | B− | Capsular polysaccharide export system | 3e-11 | 1.1235e-11 | GumB protein | COG1596 (20 proteins), periplasmic protein involved in polysaccharide export |
| TEC | 1.B.20.1.2 | XF2550 | 0 | Toxin | B− | Hemolysin secretion protein | 1e-27 | 1.5087e-22 | Outer membrane hemolysin activator protein | COG2831 (19 proteins), hemolysin activation/secretion protein |
| Secretin | 1.B.22.1.1 | XF1527 | 0 | Protein | B− | PulD protein secretin | 7e-39 | 4.0619e-25 | General secretory pathway protein D precursor | COG1450 (39 proteins), general secretory pathway protein D |
| Secretin | 1.B.22.2.1 | XF0373 | 1 | Fimbrial protein | B− | PilQ fimbrial subunit; signal peptide missing | 2e-95 | 3.8855e-52 | Fimbrial assembly protein | COG1450 (39 proteins), general secretory pathway protein D |
| Pore-forming toxins | ||||||||||
| RTX toxin | 1.C.11.1.4 | XF1011 | 2 | Pore in host | B | Bifunctional adenylate cyclase-hemolysin toxin precursor | 3e-66 | 1.7905e-14 | Hemolysin-type calcium-binding protein | COG2931 (21 proteins), RTX toxins and related Ca2+-binding proteins |
| RTX toxin | 1.C.11.1.4 | XF0668 | 0 | Pore in host | B | Bifunctional adenylate cyclase-hemolysin toxin precursor | 5e-56 | 8.5548e-14 | Hemolysin-type calcium-binding protein | COG2931 (21 proteins), RTX toxins and related Ca2+-binding proteins |
| RTX toxin | 1.C.11.1.4 | XF2407 | 0 | Pore in host | B | Bifunctional adenylate cyclase-hemolysin toxin precursor | 8e-72 | 3.6634e-11 | Bacteriocin | COG2931 (21 proteins), RTX toxins and related Ca2+-binding proteins |
| RTX toxin | 1.C.11.1.4 | XF2759 | 0 | Pore in host | B | Bifunctional adenylate cyclase-hemolysin toxin precursor | 9e-59 | 2.6427e-15 | Hemolysin-type calcium-binding protein | COG2931 (21 proteins), RTX toxins and related Ca2+-binding proteins |
Transport families and Transport Commission (TC) numbers were assigned to each Xylella protein identified by its ORF name as described in the text, following the phylogeny-based classification proposed by Saier (39). The number of TMSs for each Xylella protein was calculated using PSORT (25). Putative substrate refers to the substrate transported by the representative member of the family, as described by Saier (39). Occurrence refers to the occurrence of the family in different organisms as follows: B, bacteria; A, archaea; E, eukaryota; B−, gram-negative bacteria; B+, gram-positive bacteria; O, eukaryotic organelles; C, cyanobacteria; B-p, plasmid of gram-negative bacteria; BA?, bacteria, archaea, or perhaps eukaryota; BA, bacteria and archaea. Comments contains the name of the transport protein example having the best hit against the Xylella protein. E value is the expected value of the Blastp match between the Xylella protein and the example protein found in the present review. PRSS P value refers to the P value of the PRSS search of the corresponding Xylella protein against the example protein. Annotation refers to the original annotation of the Xylella genome (44). The COG classification refers to the Cluster of Orthologous Groups of proteins described by Tatusov et al. (46) and available at http://www.ncbi.nlm.nih.gov/COG/.
VIC, voltage-gated ion channel superfamily; MIP, major intrinsic protein; POP, Pseudomonas outer membrane porin; OOP, OmpA-OprF porin; FUP, fimbrial usher porin; AT, autotransporter; OMR, outer membrane receptor; OMF, outer membrane factor; OMA, outer membrane auxiliary protein; TEC, toxin export channel; RTX, repeat in structural toxin; EPS, exopolysaccharides.