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. 2017 Dec 11;7:503. doi: 10.3389/fcimb.2017.00503

Table 3.

Proteins with significantly altered expression in dsbA mutant compared to the FSC200 wild-type strain detected by SILAC quantitative shotgun approach.

Accessiona FTS locus tag Protein nameb up-/down-b COGc References
AFT93177 1495 Hypothetical protein, FTS_1495 up- S Straskova et al., 2009; Konecna et al., 2010; Ren et al., 2014; Qin et al., 2016
AFT93208 1538 Hypothetical protein FTS_1538 up- S Straskova et al., 2009; Konecna et al., 2010; Pávková et al., 2013; Ren et al., 2014
AFT93168 1485 Chitinase family 18 protein up- G Kadzhaev et al., 2009; Straskova et al., 2009; Chung et al., 2014; Ren et al., 2014
AFT93368 1749 Hypothetical protein FTS_1749 up- S Ren et al., 2014; Qin et al., 2016
AFT92137 0123 Pyruvate phosphate dikinase up- G
AFT92841 1034 D-alanyl-D-alanine carboxypeptidase up- M Straskova et al., 2009; Ren et al., 2014; Qin et al., 2016
AFT92421 0495 Hypothetical protein FTS_0495 up- S Ren et al., 2014
AFT93021 1279 Hypothetical protein FTS_1279 up- S Straskova et al., 2009; Chong et al., 2013; Ren et al., 2014; Qin et al., 2016
AFT93404 1789 Siderophore biosynthesis protein up- P Ramakrishnan et al., 2008; Pérez et al., 2016
AFT93162 1476 Glycerophosphoryl diester phosphodiesterase up- I Konecna et al., 2010
AFT92351 0402 Hypothetical protein FTS_0402 up- S Ren et al., 2014
AFT92903 1117 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase up- G Konecna et al., 2010; Qin et al., 2016; this study
AFT93160 1471 Catalase/peroxidase up- P Lindgren et al., 2007; Qin et al., 2016
AFT93076 1361 Parvulin-like peptidyl-prolyl isomerase domain-containing protein up- O Su et al., 2007
AFT92667 0815 Hypothetical protein FTS_0815 up- S Ren et al., 2014
AFT92381 0450 Hypothetical protein FTS_0450 up- S Brotcke et al., 2006; Brotcke and Monack, 2008; Wehrly et al., 2009
AFT92582 0702 FAD binding family protein up- C Ren et al., 2014
AFT92713 0868 X-prolyl aminopeptidase 2 up- E Guina et al., 2007
AFT93339 1709 Elongation factor Tu up- J Barel et al., 2008; Qin et al., 2016
AFT92546 0659 Hypothetical protein FTS_0659 up- S Straskova et al., 2009
AFT92986 1229 Hypothetical protein FTS_1229 up- S
AFT92133 0111/1139 Hypothetical FTS_0111 up- S Robertson et al., 2013; Bröms et al., 2016
AFT92684 0836 Isochorismatase hydrolase family protein up- Q Pavkova et al., 2006; Su et al., 2007
AFT92956 1187 Hypothetical protein FTS_1187 up- S Wehrly et al., 2009; Qin et al., 2016
AFT92755 0920 Hypothetical protein FTS_0920 up- S Brotcke et al., 2006
AFT92560 0676 Hypothetical protein FTS_0676 up- S
AFT92796 0974 Hypothetical protein FTS_0974 up-* S Ren et al., 2014
AFT92765 0935 GTP-dependent nucleic acid-binding protein EngD up-* J
AFT92195 0200 Hypothetical protein FTS_0200 down- S Dieppedale et al., 2011, 2013
AFT92865 1068 Hypothetical protein FTS_1068 down- S Straskova et al., 2009; Qin et al., 2011
AFT92060 0012 Inhibitor of RecA down- L
AFT92481 0580 Sugar porter (SP) family protein down- G
AFT93103 1397 Glycosyltransferase family protein down- M Bandara et al., 2011
AFT92194 0199 von Willebrand factor type A domain-containing protein down- R,O Dieppedale et al., 2011, 2013
AFT92732 0890 Protease, GTP-binding subunit down- J Su et al., 2007
AFT92334 0381 Type IV pili, pilus assembly protein down- N,W Salomonsson et al., 2011
AFT93371 1752 FOF1 ATP synthase subunit gamma down- C
AFT92172 0175 LPS fatty acid acyltransferase down- M McLendon et al., 2007
AFT92106 0079 Acyltransferase down- I
AFT92933 1158 Ribonuclease HII down- L Kadzhaev et al., 2009
AFT93108 1402 ABC transporter ATP-binding protein down- V Dankova et al., 2016
AFT92145 0137 Hypothetical protein FTS_0137 down- S
AFT93370 1751 FOF1 ATP synthase subunit beta down- C Qin et al., 2016
AFT93375 1756 F0F1 ATP synthase subunit C down- C
AFT93243 1582 Drug: H+ antiporter-1 (DHA1) family protein down- V Su et al., 2007
AFT93130 1439 Excinuclease ABC, subunit A down- L Su et al., 2007; Kadzhaev et al., 2009
AFT92197 0202 Hypothetical protein FTS_0202 down- S Dieppedale et al., 2011, 2013
AFT93269 1620 Nucleoside permease NUP family protein down- F
AFT92502 0602 O-antigen flippase down- C Dankova et al., 2016
AFT92502 1754 FOF1 ATP synthase subunit delta down- C
AFT93369 1750 FOF1 ATP synthase subunit epsilon down- C
AFT93467 1882 ATP-binding cassette (ABC) superfamily protein down- P,R Asare and Abu Kwaik, 2010
AFT92984 1226 ATP-dependent RNA helicase down- L
AFT93372 1753 FOF1 ATP synthase subunit alpha down- C Qin et al., 2016
AFT92658 0799 Amino acid transporter down- E Kadzhaev et al., 2009
AFT92817 1004 Radical SAM superfamily protein down- J
AFT92323 0367 Hypothetical protein FTS_0367 down- S
AFT92497 0597 Membrane protein/O-antigen protein down- M Kim et al., 2010
AFT93227 1562 Delta-aminolevulinic acid dehydratase down- H
AFT92449 0533 Uracil-DNA glycosylase down- L
AFT93102 1396 Glycosyltransferases group 1 family protein down- M Weiss et al., 2007; Bandara et al., 2011; Thomas et al., 2011
AFT92105 0078 Acyltransferase down-* I
AFT92192 0197 Uncharacterized protein FTS_0197 down-* S Dieppedale et al., 2011, 2013
a

Accession numbers and protein names according to NCBI (https://www.ncbi.nlm.nih.gov).

b

Up- or down-regulated proteins according to the following criteria: statistical significance p < 0.05; relative changes ≥ 1.5 for up-regulated or ≤ for down regulated proteins.

*

Quantified by second-level quantification workflow (extreme ratios considered).

c

Predicted function of proteins by COG using the COGnitor program (http://www.ncbi.nlm.nih.gov/COG/). S, no functional prediction; G, carbohydrate metabolism and transport; M, cell wall structure and biogenesis and outer membrane; P, inorganic ion transport and metabolism; I, lipid metabolism; O, molecular chaperons and related functions; C, energy production and conversion; E, amino acid metabolism and transport; J, translation, ribosome structure, and biogenesis; N, secretion, motility, and chemotaxis; W, extracellular structure; L, replication, recombination, and repair; V, defense mechanisms; F, nucleotide transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; H, coenzyme transport and metabolism; R, general function prediction only.

Genes encoding proteins highlighted in bold were inactivated using retargeted mobile group II introns and tested for potential attenuation in vivo.