TABLE 3.
F. psychrophilum T9SS type A CTD and type B CTD proteins identified by LC-MS/MS analysis of cell-free spent culture mediuma
| Locus tag/protein | Molecular mass (kDa)b | T9SS CTD typec | Predicted protein function or description | Spectral count of culture fluid from: |
||
|---|---|---|---|---|---|---|
| Wild type | ΔgldN mutant | ΔgldN mutant + pBFp4 | ||||
| Non-LRR T9SS CTD proteins | ||||||
| THC0290_0238/Fpp2 | 100.3 | A | Peptidase | 813 | 72 | 903 |
| THC0290_0025/SprB | 366.8 | B | Gliding motility adhesin SprB | 268 | 59 | 315 |
| THC0290_0931 | 103.2 | A | Peptidase (collagenase) | 170 | 22 | 143 |
| THC0290_2338 | 208.3 | B | Adhesin | 84 | 32 | 94 |
| THC0290_1932 | 200.0 | B | Adhesin | 48 | 17 | 36 |
| THC0290_1520 | 66.2 | A | Endonuclease | 37 | 0 | 40 |
| THC0290_2029 | 32.9 | A | 34 | 19 | 45 | |
| THC0290_1797 | 29.4 | A | 32 | 1 | 23 | |
| THC0290_1616 | 129.6 | B | Adhesin | 27 | 8 | 53 |
| THC0290_1595 | 67.9 | A | Adhesin | 24 | 8 | 16 |
| THC0290_0944 | 58.5 | A | Peptidase | 21 | 0 | 23 |
| THC0290_2146/PorU | 142.1 | A | T9SS-specific CTD peptidase | 20 | 17 | 32 |
| THC0290_1494 | 71.5 | A | Ribonuclease | 19 | 0 | 24 |
| THC0290_0332 | 269.2 | B | Adhesin | 15 | 4 | 16 |
| THC0290_1527 | 233.6 | B | Adhesin | 13 | 5 | 20 |
| THC0290_0023/SprC | 51.2 | B | Gliding motility protein SprC | 9 | 4 | 9 |
| THC0290_1047 | 87.8 | B | Adhesin | 8 | 1 | 15 |
| THC0290_1343 | 134.1 | A | Peptidase | 6 | 0 | 6 |
| THC0290_0086 | 70.9 | A | Peptidase | 6 | 0 | 9 |
| THC0290_0237/Fpp1 | 119.6 | A | Peptidase | 6 | 0 | 5 |
| THC0290_0129 | 33.6 | A | 6 | 1 | 9 | |
| THC0290_1818 | 158.9 | B | Adhesin | 6 | 0 | 6 |
| THC0290_0091 | 122.8 | A | Glycoside hydrolase | 5 | 2 | 4 |
| THC0290_1048 | 82.6 | B | Adhesin | 3 | 0 | 7 |
| THC0290_0299 | 100.1 | A | Peptidase | 1 | 16 | 6 |
| THC0290_1054 | 46.0 | A | 0 | 0 | 3 | |
| THC0290_0128 | 12.8 | A | 0 | 2 | 0 | |
| LRR proteinsd | ||||||
| THC0290_0183 | 33.2 | A | Leucine-rich repeat protein | 51 | 22 | 46 |
| THC0290_0174 | 44.5 | A | Leucine-rich repeat protein | 23 | 13 | 22 |
| THC0290_0171 | 44.5 | A | Leucine-rich repeat protein | 22 | 18 | 32 |
| THC0290_0170 | 41.7 | A | Leucine-rich repeat protein | 20 | 40 | 24 |
| THC0290_0181 | 50.1 | A | Leucine-rich repeat protein | 17 | 18 | 18 |
| THC0290_0184 | 37.0 | A | Leucine-rich repeat protein | 15 | 25 | 23 |
| THC0290_0186 | 35.3 | A | Leucine-rich repeat protein | 12 | 15 | 13 |
| THC0290_0182 | 35.0 | A | Leucine-rich repeat protein | 9 | 17 | 10 |
| THC0290_0175 | 35.3 | A | Leucine-rich repeat protein | 7 | 16 | 12 |
| THC0290_0185 | 35.3 | A | Leucine-rich repeat protein | 7 | 9 | 10 |
| THC0290_0172 | 35.2 | A | Leucine-rich repeat protein | 7 | 19 | 11 |
| THC0290_0180 | 42.1 | A | Leucine-rich repeat protein | 0 | 20 | 0 |
| THC0290_0177 | 56.0 | A | Leucine-rich repeat protein | 0 | 15 | 0 |
Proteins in cell-free culture fluid from wild-type F. psychrophilum, ΔgldN mutant, and ΔgldN mutant complemented with pBFp4 were analyzed by LC-MS/MS. Total/unweighted spectrum count corresponding to total number of spectra associated with a single protein and indicative of relative abundance of that protein is indicated for each strain. Only proteins with predicted T9SS CTDs are shown. For the full data set, which includes additional proteins, see Data Set S1 in the supplemental material. The following type A CTD proteins were not detected: THC0290_0173, THC0290_0176, THC0290_0178, THC0290_0179, THC0290_0300, THC0290_0878, THC0290_0977, THC0290_2157, and THC0290_2385. However, the LRR proteins THC0290_0173, THC0290_0176, THC0290_0178, and THC0290_0179 may have been present, because they are similar in sequence to the other LRR proteins, resulting in ambiguity regarding protein assignment for some peptides (Data Set S1). Similarly, THC0290_300 may have been missed because of similarity in sequence to THC0290_0299.
Molecular mass as calculated for full-length protein before removal of signal peptide.
Type A CTDs belong to TIGRFAM protein domain family TIGR04183. Type B CTDs belong to TIGRFAM protein domain family TIGR04131 and/or pfam13585.
These proteins have paralogs in the genome that complicate assignment of peptides.