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. 2017 Feb 5;19(1):143–157. doi: 10.1111/mpp.12507

Table 1.

Xanthomonas citri ssp. citri (XAC) periplasm‐enriched fraction proteins identified by two‐dimensional gel electrophoresis (2‐DE) followed by liquid chromatography coupled with tandem mass spectrometry (LC‐MS/MS) in non‐inducing (nutrient broth, NB) and in vitro pathogenicity‐inducing (XAM‐M) conditions (P < 0.05).

Spot Condition (more abundant spot) Open reading frame (ORF) Protein ID (exclusive peptide count)* Theoretical †
MW/pI		 Experimental ‡
MW/pI		 Mascot score Matched peptide Sequence coverage (%) Category § Cellular location Spot relative abundance (XAM‐M/NB)**
1 NB XAC0002 DNA polymerase III subunit β (0) 40.8/5.4 47.4/5.7 49 2 4 III C Unique
2 NB XAC0818 Ribokinase (2) 32.3/5.5 33.6/6.1 79 2 9 I C 0.2
3 NB XAC2546 Ketoglutarate semialdehyde dehydrogenase (2) 54.8/6.1 56.7/6.7 46 6 8 I C 0.2
4 NB XAC3556 Aminopeptidase A/I (10) 51.5/5.2 52.5/5.4 396 10 21 III C/P 0.5
XAC1204 Alanyl dipeptidyl peptidase (8) 79.7/6.2 304 11 16 III P/IM
XAC3651 ATP synthase subunit α (5) 55.4/5.3 104 9 19 I IM
XAC2378 Conserved hypothetical protein (0) 48.8/5.2 53 2 5 VIII C
5 NB XAC1838 Enolase‐phosphatase (2) 25.8/5.1 25.0/5.3 50 3 14 II U 0.4
6 NB XAC0554 Putative NADH dehydrogenase/NAD(P)H nitroreductase (5) 21.4/5.8 21.4/6.5 152 9 12 IX U 0.3
7 NB XAC1012 Outer membrane protein (12) 40.0/4.6 34.4/4.2 177 10 26 IV OM 0.2
XAC3556 Aminopeptidase A/I (2) 51.5/5.2 104 2 5 III C/P
XAC0104 Metalloprotease (2) 37.8/4.8 43 2 3 III S
8 NB XAC1078 ATP‐dependent Clp protease proteolytic subunit (13) 22.8/5.4 236 16 46 III C 0.4
XAC2067 Keto‐hydroxyglutarate‐aldolase/keto‐deoxy‐phosphogluconate aldolase (2) 22.9/5.2 23.0/5.3 37 4 28 I C
9 NB XAC1012 Outer membrane protein (18) 39.6/4.6 40.9/4.2 423 18 44 IV OM 0.3
10* NB XAC0957 Elongation factor Tu 43.3/5.5 498 20 28 III C 0.2
XAC1348 Acetoacetyl‐CoA thiolase 40.1/6.3 25.5/5.8 229 7 16 II P/IM
XAC0868 Hypothetical protein XAC0868 28.2/9.1 92 4 12 VIII P/S
11* NB XAC0541 10‐kDa chaperonin (9) 10.0/5.8 11.0/6.0 238 13 94 III C 0.3
12* NB XAC0542 60‐kDa chaperonin (32) 57.1/5.1 58.6/5.2 2584 58 68 III C 0.8
13 XAM‐M XAC3345 Pyruvate kinase type II 54.1/5.6 58.6/5.8 42 2 1 I U Unique
14 XAM‐M XAC0823 Outer membrane hemin receptor 86.2/6.2 75.0/5.5 23 3 3 V OM Unique
15* XAM‐M XAC0025 Xanthomonas conserved hypothetical protein 22.2/5.7 22.3/5.6 347 11 22 VIII P 2.5
XAC3583 dTDP‐4‐dehydrorhamnose‐3,5‐epimerase 20.5/5.4 153 6 25 IV U
16 XAM‐M XAC3442 Inorganic pyrophosphatase 19.9/4.9 21.6/4.8 213 9 28 I C Unique
XAC0296 Monoxygenase 52.3/7.9 24 2 1 I U
17 XAM‐M XAC0470 Phosphoribosylaminoimidazole‐succinocarboxamide synthase 34.6/5.2 32.7/5.3 46 4 10 II C 16.2
XAC1421 Elongation factor Ts 31.1/5.2 46 2 6 III C
18 XAM‐M XAC3352 Glyceraldehyde‐3‐phosphate dehydrogenase 36.2/6.0 404 25 45 I C/S 3.7
XAC0124 Fructose‐1,6‐bisphosphatase class 1 36.8/5.7 80 5 19 I C
XAC4367 Glycerophosphoryl diester phosphodiesterase 39.8/6.0 37.2/6.2 72 4 13 III P
XAC2638 Hypothetical protein 37.2/6.2 20 2 3 VIII U
19 XAM‐M XAC0120 TldD protein 48.8/6.0 49.1/6.3 94 4 6 III C Unique
XAC3352 Glyceraldehyde‐3‐phosphate dehydrogenase 36.2/6.0 43 2 4 I C
20 XAM‐M XAC0865 Peptidyl‐prolyl cis–trans‐isomerase 50.1/5.4 941 36 38 III P Unique
XAC0120 TldD protein 48.8/6.0 48.5/5.3 112 2 6 III C
XAC3851 Conserved hypothetical protein 50.0/5.3 104 3 5 VIII U
21 XAM‐M XAC0865 Peptidyl‐prolyl cis–trans‐isomerase 50.1/5.4 293 13 25 III P Unique
XACb0007/XAC3225 Lytic murein transglycosylase/transglycosylase 46.2/5.9 44.3/5.3 293 10 14 IV IM
XAC3851 Conserved hypothetical protein 50.0/5.3 129 5 11 VIII U
XAC2965 UDP‐N‐acetylglucosamine 1‐carboxyvinyltransferase 44.6/5.3 69 4 7 IV C
22* XAM‐M XAC3352 Glyceraldehyde‐3‐phosphate dehydrogenase (9) 36.2/6.0 742 40 47 I C/S 2.9
XACb0007/XAC3225 Lytic murein transglycosylase/transglycosylase (0) 46.2/5.9 37.0/6.6 230 8 25 IV IM
XAC0865 Peptidyl‐prolyl cis–trans‐isomerase (0) 50.1/5.4 43 2 6 III P
23 XAM‐M XAC0542 60‐kDa chaperonin (10) 57.1/5.1 61.8/6.5 580 15 25 III C Unique
24 XAM‐M XAC0542 60‐kDa chaperonin (4) 57.1/5.1 59.3/5.6 91 3 10 III C Unique
25 XAM‐M XAC0542 60‐kDa chaperonin (2) 57.1/5.1 59.1/5.7 59 2 10 III C Unique
26 XAM‐M XAC3141 Outer membrane protein P6 precursor (6) 19.8/7.6 19.2/4.9 110 8 43 IV OM Unique
XAC3510 Peptide deformylase (0) 19.2/4.8 42 2 8 III U
27 XAM‐M XAC3584 Glucose‐1‐phosphate thymidylyltransferase (7) 34.1/5.8 29.4/5.8 138 8 26 IV C Unique
XAC1321 Periplasmic protease (6) 53.9/7.8 118 7 17 III P
28 XAM‐M XAC1017 ABC transporter sulfate‐binding protein (2) 37.8/6.7 33.0/6.7 93 2 5 V P 9.0
29 XAM‐M XAC3141 Outer membrane protein P6 precursor (6) 19.8/7.6 18.9/4.6 90 8 43 IV OM Unique
30 XAM‐M XAC3372 Transketolase 1 (6) 72.7/5.6 69.8/6.1 114 5 7 I C 9.2
31 XAM‐M XAC2386 Superoxidase dismutase (12) 22.7/5.5 23.0/5.7 303 16 71 VII P/S 1.8
32 XAM‐M XAC1321 Periplasmic protease (2) 53.9/7.8 29.8/6.2 74 2 4 III P 2.2
33 XAM‐M XAC3579 Phosphoglucomutase (8) 49.3/5.2 46.5/5.3 146 8 26 VII C Unique
XACb0007/XAC3225 Lytic murein transglycosylase/transglycosylase (3) 46.2/5.9 123 5 10 IV IM
34 XAM‐M XAC1421 Elongation factor Ts (4) 31.1/5.2 36.7/5.3 89 4 10 III C Unique
35 XAM‐M XAC2999 Peptidase (2) 79.2/5.8 70.4/5.7 63 4 4 III S 6.1
36 XAM‐M XAC1434 Hypothetical protein XAC1434 (9) 38.7/5.9 34.7/6.2 159 10 29 VIII P 6.6
37 XAM‐M XAC1262 Conserved hypothetical protein (3) 63.4/5.9 67.7/6.4 67 5 9 VIII S 2.3
38 XAM‐M XACb0007/XAC3225 Lytic murein transglycosylase/transglycosylase (4) 46.2/5.9 43.8/5.8 140 6 10 IV IM 6.6
39 XAM‐M XAC3649 ATP synthase subunit β (3) 51.0/5.2 54.0/5.2 74 4 7 I IM Unique
XAC0542 60‐kDa chaperonin (3) 57.1/5.1 65 2 4 III C
40 XAM‐M XAC3235 Succinyl‐CoA synthetase subunit α (11) 29.8/6.4 18.6/6.9 336 12 37 I C/S 2.7
41 XAM‐M XAC3309 Aminopeptidase 48.9/5.9 49.2/6.2 386 22 43 III S 15.3
XAC0120 TldD protein 48.8/6.0 41 2 4 III C
42 XAM‐M XACb0007/XAC3225 Lytic murein transglycosylase/transglycosylase (11) 46.2/5.9 42.9/5.6 522 17 24 IV IM 163.3
XAC0002 DNA polymerase III subunit β (2) 40.8/5.4 48 2 4 III C

*Proteins identified using the Mascot/XAC database and National Center for Biotechnology Information (NCBI); in parentheses are indicated the exclusive peptide counts determined for some spots using the software Scaffold™ (Proteome Software Inc., Portland, OR, USA) for 100% protein identification probability. Spots with asterisks (10, 11, 12, 15, 22) were isolated from both NB and XAM‐M conditions (as determined by ImageMaster 2D Platinum software, GE Healthcare, Uppsala, Sweden) and the same protein (in bold) was identified for both spots.

†Theoretical MW/pI obtained from the NCBI database.

‡Experimental MW/pI calculated from the position on the two‐dimensional gel by Image Master Platinum software (GE Healthcare).

§Protein clusters according to their annotated function (da Silva et al., 2002).

Predicted cellular location of proteins by PredSi, SignalP 2.0 and SecretomeP 2.0. P, C, IM and OM correspond to periplasm, cytoplasm, inner membrane and outer membrane, respectively. U, unknown, could not be identified. S is used for proteins secreted to the extracellular medium as suggested by SecretomeP 2.0.

**Relative abundance (arbitrary units) for matched spots was calculated as the ratio of the volume percentage average of pathogenicity‐inducing (XAM‐M medium) and pathogenicity‐non‐inducing (NB medium) conditions. ‘Unique’ spots were detected in only one of the two conditions (NB or XAM‐M).