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Table 1 Differentially expressed genes in acid-adapted E. coli O157:H7 ATCC 43889 compared to corresponding non-adapted strains

From: Transcriptome changes and polymyxin resistance of acid-adapted Escherichia coli O157:H7 ATCC 43889

Regulation Rank length (bp) Fold change log2 ratio p-value Gene symbol Product Functional categorya
Up 1 189 4.95 0.02 RS05560 Cell division inhibition protein DicB Biological process: single-organism process, cellular process, biological regulation
2 564 4.95 0.02 RS06705 Terminase small subunit Biological process: cellular process
3 207 3.72 0.08 RS05320 Phage tail protein Cellular component: membrane,
4 2124 3.72 0.08 RS27375 Terminase Molecular function: binding
5 366 3.61 0.02 RS28370 HNH endonuclease Biological process: metabolic process
Molecular function: catalytic activity
6 1674 3.23 0.01 kdpA Potassium-transporting ATPase A chain Biological process: localization, organism process
Cellular component: membrane part, membrane, cell part
Molecular function: transporter activity, binding, catalytic activity
7 147 3.23 0.02 RS06750 Hypothetical protein No hit
8 261 2.63 0.03 bhsA Multiple stress resistance protein BhsA precursor Biological process: metabolic process, single-organism process, cellular process, response to stimulus
Cellular component: membrane part, cell part
9 108 2.61 0.03 RS08170 Stress-induced bacterial acidophilic repeat motif protein Biological process: unclassified
Cellular component: unclassified
Molecular function: unclassified
10 1491 2.54 0.03 patA Putrescine aminotransferase Biological process: metabolic process, cellular process
Cellular component: cell part
Molecular function: binding, catalytic activity
11 243 2.39 0.05 RS16110 Polysaccharide production threonine-rich protein No hit
12 468 2.27 0.08 RS27360 Endopeptidase Biological process: cellular process
13 183 2.20 0.07 RS06135 Stress-induced bacterial acidophilic repeat motif protein Biological process: unclassified
Cellular component: unclassified
Molecular function: unclassified
14 309 2.16 0.09 RS04915 Phage tail assembly protein T No hit
15 141 2.15 0.08 RS25935 Hok/gef family protein Cellular component: membrane
16 430 2.15 0.08 ibpB Small heat shock protein IbpB Biological process: response to stimulus
Cellular component: cell part
Molecular function: binding
17 96 2.09 0.09 RS03750 Hypothetical protein No hit
18 132 2.07 0.11 RS26305 Hypothetical protein No hit
19 1983 2.05 0.10 arnA Bifunctional polymyxin resistance protein ArnA Biological process: metabolic process, response to stimulus, single-organism process, cellular process
Molecular function: binding, catalytic activity
20 213 2.03 0.10 RS00040 Hypothetical protein No hit
Down 1 222 −6.75 0.01 RS26915 TraR/DksA family transcriptional regulator Biological process: biological regulation
2 246 −4.52 0.07 RS27335 Hypothetical protein No hit
3 366 −4.21 0.01 RS03415 HNH endonuclease Biological process: metabolic process
Molecular function: catalytic activity
4 1341 −4.20 0.00 lamB Maltoporin precursor Biological process: localization, response to stimulus, multi-organism process, single-organism process, cellular process
Cellular component: membrane part, membrane, macromolecular complex, cell part
Molecular function: molecular transducer activity, transporter activity, binding
5 921 −3.17 0.01 malM Maltose operon protein MalM Biological process: localization, single-organism process
Cellular component: cell part
6 750 -3.03 0.01 invF Invasion protein InvF Biological process: biological regulation
Molecular function: nucleic acid binding transcription factor activity
7 351 −3.03 0.01 RS15960 Hypothetical protein Biological process: response to stimulus
8 228 −2.92 0.07 RS03410 DUF3950 domain-containing protein No hit
9 285 −2.92 0.02 RS15965 Hypothetical protein No hit
10 1116 −2.81 0.02 malK Maltose/maltodextrin import ATP-binding protein MalK Biological process: localization, single-organism process
Cellular component: membrane part, membrane, macromolecular complex, cell part
Molecular function: transporter activity,
binding, catalytic activity
11 333 −2.79 0.02 RS14560 DUF2686 family protein No hit
12 360 −2.78 0.02 RS15860 Hypothetical protein No hit
13 1191 −2.72 0.02 malE Maltose-binding periplasmic protein precursor Biological Process: localization, response to stimulus, single-organism process, - locomotion, cellular process
Cellular component: membrane part, macromolecular complex, cell part
Molecular function: transporter activity, binding
14 1416 −2.71 0.02 tnaA Tryptophanase Biological process: metabolic process, single-organism process, cellular process
Cellular component: membrane, cell part
Molecular function: binding, catalytic activity
15 927 −2.63 0.03 coaA_1 Pantothenate kinase Biological process: metabolic process, single-organism process, cellular process
Cellular component: cell part
Molecular function: binding, catalytic activity
  1. aFunctional categories were based on GO analysis classifications were based on annotation from the E. coli best-hit gene models (E value ≤ 10–5) and GO analysis search using the BLAST2GO program