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

Hwang, Daekeun; Kim, Seung Min; Kim, Hyun Jung

doi:10.1186/s13099-020-00390-5

Gut Pathogens

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 category^a
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
	5	366	3.61	0.02	RS28370	HNH endonuclease	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
	8	261	2.63	0.03	bhsA	Multiple stress resistance protein BhsA precursor	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
	19	1983	2.05	0.10	arnA	Bifunctional polymyxin resistance protein ArnA	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
	3	366	−4.21	0.01	RS03415	HNH endonuclease	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
	5	921	−3.17	0.01	malM	Maltose operon protein MalM	Cellular component: cell part
	6	750	-3.03	0.01	invF	Invasion protein InvF	Biological process: biological regulation
	6	750	-3.03	0.01	invF	Invasion protein InvF	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

^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

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ISSN: 1757-4749

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