Table 1.
Identification of the 2‐DE secretome changes between the selected Propionibacterium freudenreichii cereal (JS14) and dairy (JS22) strains
| Spota | Protein | Locus_Tag | More in | Fold‐changeb | Mw (Da)c | pIc | [ms] ID score (P < 0.05)d | Seq. cov. (%)d | No. pept.d | PPe | Sig. pept.e | TMDe | NC‐Secr.e |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Surface proteins | |||||||||||||
| 1–4 | Surface‐anchored fimbrial subunit (FimB) | PFR_JS14_352 | JS14 | 3.1, 6.7, 6.9, 2.3 | 98 347 | 5.8 | 258, 247, 432, 186 | 8.5, 8.5, 12, 8.8 | 7, 7, 9, 6 | Yes | No | 1 | Yes |
| 5, 6, 8, 9, 12 | Internalin A (InlA, fragment; LRRs, no SLHs) | PFR_JS22_1_2260 | JS22 | 3.1, 6.7, 8.9, 3.5 | 61 422 | 5.2 | 1199, 2960, 481, 5294, 833 | 22.1, 29, 12, 36, 12.5 | 18, 80, 9, 104, 10 | Yes | Yes | 1 | No |
| 8, 9 | Surface layer protein A (SIpA; SLH domain) | PFR_JS22_1_534 | JS22 | 8.9, 3.5 | 58 552 | 4.7 | 2369, 2642 | 35, 44 | 48, 68 | Yes | Yes | No | No |
| 8 | SIpA (SLH domain) | PFR_JS22_1_535 | JS22 | 8.9 | 50 562 | 4.8 | 150 | 6 | 6 | No | No | No | Yes |
| 27 | S‐layer domain protein (SLH) | PFR_JS14_687 | JS14 | 2.2 | 23 620 | 8.4 | 267 | 28.3 | 11 | No | Yes | No | No |
| 12–14, 17 | S‐layer domain protein (SLH; no evolutionary counterpart in JS14) | PFR_JS22_1_537 | JS22 | 3.5, 15.3, 6.6, 3.2 | 32 959 | 5.0 | 170, 3348, 851, 270 | 12, 25, 17, 15.5 | 3, 76, 20, 3 | Yes | Yes | 1 | No |
| 12 | Hypothetical secreted protein (YkuD superfamily domain) | PFR_JS22‐1_1900 | JS22 | 3.5 | 30 445 | 4.9 | 93 | 9.4 | 3 | No | Yes | 1 | No |
| 10 | d‐alanyl‐d‐alanine carboxypeptidase, serine type | PFR_JS22‐1_347 | JS22 | 3.9 | 41 835 | 4.7 | 1283 | 22.8 | 30 | Yes | Yes | 1 | No |
| 10 | Peptidase M23B family/metalloendo‐peptidase | PFR_JS22‐1_759 | JS22 | 3.9 | 39 104 | 5.2 | 121 | 5.9 | 2 | No | Yes | 1 | No |
| 11 | d‐alanyl‐d‐alanine carboxypeptidase, serine type | PFR_JS14_299 | JS14 | 5.2 | 41 835 | 5.0 | 1383 | 22.8 | 34 | Yes | Yes | 1 | No |
| 11 | Peptidase M23B family/metalloendo‐peptidase | PFR_JS14_718 | JS14 | 5.2 | 39 104 | 5.2 | 107 | 5.9 | 2 | No | Yes | 1 | No |
| Secreted proteins | |||||||||||||
| 17, 24 | RpfB | PFR_JS22_1_1666 | JS22 | 3.2, 2.4 | 37 701 | 5.3 | 1445, 400, 134 | 48.8, 29.9 | 39, 7 | Yes | Yes | 1 | No |
| 15, 18–20, 22, 23, 26 | Resuscitation‐promoting factor RpfB | PFR_JS14_1610 | JS14 | 4.6, 3.2, 4.7, 3.3, 2.9, 5.4, 3.4 | 37 701 | 5.27 | 2232, 444, 562, 597, 557, 3122, 134, 3077 | 36, 29.6, 23.3, 24.4,35, 30.7, 18 | 59,10, 13, 19, 12, 76, 75, 4 | Yes | Yes | 1 | No |
| 8, 9 | NlpC/P60 family secreted peptidase | PFR_JS22‐1_1785 | JS22 | 8.9, 3.5 | 59 700 | 4.8 | 423, 475 | 17, 17 | 8, 8 | No | Yes | No | No |
| 12 | ABC‐type amino acid transport system, secreted component | PFR_JS22‐1_90 | JS22 | 3.5 | 31 672 | 4.8 | 149 | 42 620 | 2 | No | Yes | No | No |
| 6 | Oligopeptide‐binding protein OppA | PFR_JS22‐1_1684 | JS22 | 6.7 | 61 589 | 5.1 | 79 | 5.4 | 2 | Yes | Yes | No | No |
| 7 | Oligopeptide‐binding protein OppA | PFR_JS14_1627 | JS14 | 2.1 | 61 589 | 5.7 | 1200 | 32 | 31 | Yes | Yes | No | No |
| 21 | Putative peptidoglycan‐binding protein, cell‐wall catabolism | PFR_JS22‐1_2177 | JS22 | 2.6 | 20 157 | 4.8 | 511 | 51 | 7 | No | Yes | No | No |
| Cytoplasmic proteins | |||||||||||||
| 5 | 60 kDa chaperonin 1 (GroEL) | PFR_JS22‐1_1630 | JS22 | 3.1 | 56 169 | 4.7 | 2544 | 48.9 | 60 | Yes | No | No | Yes |
| 16 | Hypothetical protein (Big2 family) | PFR_JS22‐1_26 | JS22 | 5.7 | 30 145 | 4.7 | 375 | 42 607 | 9 | No | No | No | Yes |
| 21 | Protein of hypothetical function DUF162 | PFR_JS22‐1_517 | JS22 | 2.6 | 23 227 | 4.7 | 292 | 39 | 6 | No | No | No | No |
| Putative electron transfer flavoprotein FixA | PFR_JS22‐1_2035 | JS22 | 2.6 | 25 770 | 4.7 | 136 | 17 | 3 | No | No | No | No | |
Spot numbers correspond to those in Fig. 5. In some cases, several proteins were identified in one spot; thus, the change in average volume ratio is linked to one or combination of the identified proteins.
The spots displaying > 2.0‐fold change (P < 0.05) in spot volume values in each four replicate 2‐DE gels within both test groups were picked for LC‐MS/MS identification.
Theoretical Mw (kDa) and pI values obtained from MASCOT search results.
Mascot identification scores (P < 0.05) derived from Mascot search. No. pept., number of matched peptides. Seq. cov., sequence coverage.
PP, Presence of phosphorylated peptides; Sig. pept., presence of signal peptide; TMD, presence of transmembrane domain(s), NC‐Secr., non‐classically secreted protein. SignalP4.1 (http://www.cbs.dtu.dk/services/SignalP-4.1/) was used to indicate proteins that are exported out of the cells via the Sec‐ (Petersen et al., 2011) or TatP‐ (http://www.cbs.dtu.dk/services/TatP/) dependent pathways (Bendtsen et al., 2005). secretomep 2.0 (http://www.cbs.dtu.dk/services/SecretomeP/) was used to predict proteins (moonlighting proteins) that are exported out of the cells via signal‐peptide‐independent or non‐classical secretion mechanisms (Bendtsen et al., 2005). TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) (Krogh et al., 2001) was used to indicate the number of probable trans‐membrane‐helices/domains (TMD).