TABLE 2.
Summary of proteins with a decreased abundance in the spy null strain
| Protein | Fold change (×) | P | Identified comparison group | Topology classa | Description |
|---|---|---|---|---|---|
| OmpC | 29.6 | 0.002 | L32P/Δspy | Outer membrane β-barrel protein | Outer membrane pores allowing for small molecular diffusion |
| 16.3 | 0.003 | Q100L/Δspy | Outer membrane β-barrel protein | Outer membrane pores allowing for small molecular diffusion | |
| OmpX | 2.1 | 0.013 | L32P/Δspy | Outer membrane β-barrel protein | Related to type 1 fimbriae production; biofilm formation and invasion of pathogenic E. coli |
| OmpT | 3.6 | 0.004 | WT/Δspy | Outer membrane β-barrel protein | Protease |
| DacA | 12.9 | 0.021 | Q100L/Δspy | Periplasmic protein | Carboxypeptidase involved in peptidoglycan biosynthesis |
| YaeQ | 2.7 | 0.028 | Q100L/Δspy | Cytoplasmic protein | Uncharacterized |
| YeeN | 2.7 | 0.003 | Q100L/Δspy | Cytoplasmic protein | Regulation of transcription |
| CopA | 2.5 | 0.013 | Q100L/Δspy | Integral inner membrane protein | Copper-exporting P-type ATPase |
| PpiB | 1.9 | 0.016 | Q100L/Δspy | Peripheral inner membrane protein facing the cytoplasm | Peptidyl-prolyl cis-trans isomerase |
| MsrB | 2.4 | 0.030 | L32P/Δspy | Cytoplasmic protein | Peptide methionine sulfoxide reductase |
| YkgE | 2.8 | 0.016 | WT/Δspy | Cytoplasmic protein | Uncharacterized |
| LamBc | 149.6b | 5.01E-05 | Q100L/Δspy | Outer membrane β-barrel protein | Maltose and maltodextrins transportation |
| FimHc | 127.0b | 0.001 | WT/Δspy | Fimbrium | Regulation of length and mediation of adhesion of type 1 fimbriae |
| SufAc | 78b | 5.54E-08 | L32P/Δspy | Peripheral inner membrane protein facing the cytoplasm | Iron-sulfur cluster assembly |
| PmrDc | 167.8b | 1.63E-04 | WT/Δspy | Cytoplasmic protein | Mediate transcriptional induction of BasR-activated genes to induce polymyxin resistance |
| YjjXc | 62.4b | 4.51E-06 | WT/Δspy | Cytoplasmic protein | Inosine/xanthosine triphosphatase |
| YggUc | 15.6b | 2.85E-04 | WT/Δspy | Cytoplasmic protein | Uncharacterized |
| SufEc | 27.9b | 1.96E-05 | WT/Δspy | Peripheral inner membrane protein facing the cytoplasm | Cysteine desulfuration |
| 18.2b | 9.31E-06 | L32P/Δspy | |||
| 35.9b | 4.64E-05 | Q100L/Δspy |
a
The topology class of each protein was noted according to subcellular topology and localization of the Escherichia coli polypeptides (STEPdb).
b
The missing label-free quantification (LFQ) values were imputed using deterministic minimal imputation (58), as described in the supplemental materials and methods in Text S1.
c
Fold change absent in Δspy.