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. 2018 Dec 12;13(12):e0207161. doi: 10.1371/journal.pone.0207161

Table 3. Significant protein differences in SA564-ΔccpA relative to SA564-ΔhptRS/ccpA.

Three Way Interaction (s x m x h)
Protein CcpA Regulated E.C. Protein Function Peptides/Protein FC TSB 2h FC TSB 6h FC TSB-dex 2h FC TSB-dex 6h
CLPL_STAAM ATP-dependent Clp protease 60 0.998 1.396 0.938 1.651
DHA1_STAAM * EC:1.4.1.1 Alanine dehydrogenase 7 0.944 1.276 1.096 2.550
LDH2_STAAM EC:1.1.1.27 L-lactate dehydrogenase 2 42 1.114 2.427 1.206 1.478
OTC_STAAM *** EC:2.1.3.3 Ornithine transcarbamoylase 5 1.024 1.568 1.128 2.291
PFLB_STAAM *** EC:2.3.1.54 Formate C-acetyltransferase 146 1.049 2.765 1.136 1.908
IDH_STAAM *** EC:1.1.1.42 Isocitrate dehydrogenase 64 0.693 0.635 0.749 0.869
SYS_STAAM EC:6.1.1.11 Seryl-tRNA synthetase 69 1.019 1.011 1.119 0.703
Two Way Interaction (s x h)
Protein CcpA Regulated E.C. Protein Function Peptides/Protein FC 2h FC 6h
Y840_STAAM Uncharacterized protein SAV0840 32 1.328 1.712
ADH_STAAM * EC:1.1.1.1 Alcohol dehydrogenase 41 1.009 2.241
ASP23_STAAM Alkaline shock protein 23 52 1.416 1.723
DAPH_STAAM EC:2.3.1.89 Tetrahydrodipicolinate N-acetyltransferase 2 1.026 1.897
SBI_STAAM * Immunoglobulin-binding protein 9 1.002 1.532
OHRL_STAAM Organic hydroperoxide resistance protein-like 3 1.158 2.595
ACKA_STAAM * EC:2.7.2.1 Acetate kinase 73 1.172 1.489
Y1710_STAAM Putative universal stress protein SAV1710 30 1.102 1.617
Y1625_STAAM Uncharacterized protein SAV1625 20 1.717 2.095
SYG_STAAM EC:6.1.1.14 Glycyl-tRNA synthetase 52 0.967 0.769
PCKA_STAAM *** EC:4.1.1.49 Phosphoenolpyruvate carboxykinase 73 1.008 0.778
TKT_STAAM EC:2.2.1.1 Transketolase 84 0.821 0.697
FTHS_STAAM *** EC:6.3.4.3 Formyltetrahydrofolate synthetase 87 0.857 0.672
FOLD_STAAM * EC:1.5.1.5 Methylenetetrahydrofolate dehydrogenase 48 0.936 0.790
ENO_STAAM * EC:4.2.1.11 2-phospho-D-glycerate hydro-lyase 78 0.806 0.740
TPX_STAAM EC:1.11.1.15 Probable thiol peroxidase 27 0.794 0.553
G6PI_STAAM EC:5.3.1.9 Glucose-6-phosphate isomerase 77 0.896 0.738
Main Effect (s)
Protein CcpA Regulated E.C. Protein Function Peptides/Protein FC
DNAK_STAAM Chaperone protein 151 1.216
EFG_STAAM Elongation factor G 173 1.111
IMDH_STAAM * EC:1.1.1.205 Inosine-5'-monophosphate dehydrogenase 125 1.197
MQO2_STAAM EC:1.1.5.4 Probable malate:quinone oxidoreductase 2 125 1.159
QOX2_STAAM EC:1.10.3.12 Probable quinol oxidase subunit 2 45 1.238
RSBW_STAAM * EC:2.7.11.1 Serine-protein kinase RsbW 2 1.227
SARS_STAAM * HTH-type transcriptional regulator 6 1.640
SODM2_STAAM * EC:1.15.1.1 Superoxide dismutase 10 1.660
ALDA_STAAM *** EC:1.2.1.3 Putative aldehyde dehydrogenase 88 0.784
CRTN_STAAM EC:1.3.8.2 Dehydrosqualene desaturase 2 0.684
CYSK_STAAM EC:2.5.1.47 Cysteine synthase 66 0.798
DBH_STAAM DNA-binding protein HU 46 0.714
DEOC2_STAAM EC:4.1.2.4 Deoxyribose-phosphate aldolase 2 41 0.824
DNLJ_STAAM EC:6.5.1.2 DNA ligase 7 0.450
FEMA_STAAM EC:2.3.2.17 Aminoacyltransferase 2 0.654
GLYA_STAAM EC:2.1.2.1 Serine hydroxymethyltransferase 58 0.839
ISPD2_STAAM EC:2.7.7.40 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2 18 0.817
MURA2_STAAM EC:2.5.1.7 UDP-N-acetylglucosamine 1-carboxyvinyltransferase 2 11 0.784
RS1_STAAM 30S ribosomal protein S1 58 0.746
THIO_STAAM Thioredoxin 46 0.777
THLA_STAAM Probable acetyl-CoA acyltransferase 32 0.818
Y2578_STAAM HTH-type transcriptional regulator 2 0.753
Y968_STAAM Uncharacterized protein SAV0968 44 0.791

***—Bioinformatically Identified and Experimentally Verified as CcpA regulated [8, 18]

**—Bioinformatically Identified as CcpA regulated through Regprecise database [18]

*—Experimentally Identified as CcpA regulated [8]

Cells with diagonal line backgrounds = Not Significant

Cells with bold borders = Significant (p ≤ 0.05)

FC—Fold Change