. 2023 Sep 13;67(10):e00111-23. doi: 10.1128/aac.00111-23

TABLE 3.

List of differentially expressed genes from UB12-TC clones compared to UB12-RC recipient strain ^a

UB12-RC					UB12-TC		UB12-TC^ive.1		UB12-TC^ive.3		UB12-TCΔpIncI.1
Genome reference	Locus reference	Gene	Product	GO terms^b	log2FC	P _adj	log2FC	P _adj	log2FC	P _adj	log2FC	P _adj
ECOL4764K	85852650	cheA	Chemotaxis protein CheA	Chemotaxis (NT)	2,44784	0,00238	1,66181	0,02643	1,61793	0,05792	3,39695	3,1E-17
ECOL4764K	85852652	tar	Methyl-accepting chemotaxis protein Tar	Chemotaxis (NT)	0,35905	0,99976	0,90038	0,56711	1,08194	0,12425	2,52615	1,8E-09
ECOL4764K	85852654	cheR	Chemotaxis protein methyltransferase	Chemotaxis (J)	1,31467	0,99976	0,53732	0,99727	0,74834	0,94242	1,94461	2,6E-05
ECOL4764K	85852655	cheB	Protein-glutamate methylesterase/protein glutamine deamidase	Chemotaxis (NT)	1,61018	0,86086	1,95395	0,00039	1,90874	0,0255	3,37828	4,9E-13
ECOL4764K	85852656	cheY	Chemotaxis protein CheY	Chemotaxis (KT)	−0,386	0,99976	0,84639	0,72816	0,84993	0,41767	1,44826	0,00534
ECOL4764K	85852657	cheZ	Chemotaxis protein CheZ	Chemotaxis (J)	0,14321	0,99976	0,47045	0,99727	0,53222	0,99983	1,46782	0,01351
ECOL4764K	85853147	trg	Methyl-accepting chemotaxis protein Trg	Chemotaxis (NT)	0,22622	0,99976	0,47636	0,99727	0,34401	0,99983	1,32684	0,01396
ECOL4764K	85852653	tap	Methyl-accepting chemotaxis protein Tap	Chemotaxis (NT)	1,64986	0,27944	1,79255	0,00465	1,92087	0,00359	3,55573	1,2E-20
ECOL4764K	85852566	yeeN	Putative transcriptional regulator YeeN	Function unknown (K)	1,56735	0,18152	1,87188	0,08396	1,94558	0,01514	1,2682	0,99982
ECOL4764K	85851949		Protein of unknown function	Function unknown (S)	1,18937	0,64644	0,95973	0,3662	1,05386	0,0478	0,54491	0,99982
ECOL4764K	85852023		Conserved protein of unknown function	Function unknown (S)	1,0608	0,72326	1,91186	0,12351	1,61571	0,03232	0,69775	0,99982
ECOL4764K	85852530	yeeX	DUF496 domain-containing protein YeeX	Function unknown (S)	1,48447	0,12054	1,32007	0,00832	1,55266	0,00204	1,26712	0,42012
ECOL4764K	85853785		SIR2_2 domain-containing protein	Function unknown (S)	1,78236	0,05217	2,05694	0,00026	2,08265	3,5E-05	1,6974	0,99982
ECOL4764K	85854633	yjcZ	Uncharacterized protein YjcZ	Function unknown (S)	1,01766	0,99976	0,54035	0,99727	0,85744	0,39624	2,44203	0,0003
ECOL4764K	85854701		YjbI protein	Function unknown (S)	−0,9134	0,99976	2,28377	0,03834	2,27538	0,05809	0,7817	0,99982
ECOL4764K	85854863	ybdZ	Enterobactin biosynthesis protein YbdZ	Function unknown (S)	−2,2921	0,99976	3,13395	0,02211	1,40956	0,22322	0,91143	0,99982
ECOL4764K	85851865	srlA	Sorbitol-specific PTS enzyme IIC2 component	Metabolism (G)	0,4513	0,99976	1,62365	0,99727	1,27625	0,03441	1,14754	0,81138
ECOL4764K	85852338	napD	NapA signal peptide-binding chaperone NapD	Metabolism (P)	0,82012	0,99976	2,2929	0,056	2,87501	0,00812	2,25275	0,06792
ECOL4764K	85853341	narK	Nitrate:nitrite antiporter NarK	Metabolism (P)	−0,3839	0,99976	1,057	0,97335	2,61826	0,04322	1,92704	0,78516
ECOL4764K	85854703	lamB	Maltose outer membrane channel/phage lambda receptor protein	Metabolism (M)	−0,332	0,99976	3,02916	0,03104	2,854	0,01182	1,67913	0,99982
ECOL4764K	85854704	malK	Maltose ABC transporter ATP binding subunit	Metabolism (P)	−0,9127	0,99976	2,91751	0,00246	2,87201	0,00369	1,26125	0,01394
ECOL4764K	85854705	malE	Maltose ABC transporter periplasmic binding protein	Metabolism (P)	−0,0777	0,99976	2,29064	0,05361	2,32236	0,03579	1,12427	0,06162
ECOL4764K	85854706	malF	Maltose ABC transporter membrane subunit MalF	Metabolism (G)	0,13807	0,99976	2,87309	0,00955	2,83601	0,01087	1,03171	0,41672
ECOL4764K	85853611	gnsA	Putative phosphatidylethanolamine synthesis regulator GnsA	Metabolism (S)	1,94991	0,01334	1,62445	0,56803	1,48141	0,4418	0,75222	0,99982
ECOL4764K	85852618	fliS	Flagellar biosynthesis protein FliS	Mobility (N)	−0,3836	0,99976	1,10601	0,47705	1,05056	0,31126	1,59581	0,00036
ECOL4764K	85852620	fliC	Flagellar filament structural protein	Mobility (N)	1,27948	0,36049	1,36333	0,00715	1,47471	0,00223	2,6014	6,3E-11
ECOL4764K	85852648	motA	Motility protein A	Mobility (N)	2,39223	0,01244	2,45117	2,1E-06	2,67929	5,7E-11	4,82804	5,9E-22
ECOL4764K	85852649	motB	Motility protein B	Mobility (N)	1,88766	0,12858	1,62233	0,0069	1,54818	0,02353	3,54867	6,12E-19
ECOL4764K	85853521	flgL	Flagellar hook-filament junction protein 2	Mobility (N)	0,27039	0,99976	0,61263	0,99727	0,5725	0,99983	1,70499	1,9E-05
ECOL4764K	85853522	flgK	Flagellar hook-filament junction protein 1	Mobility (N)	0,10274	0,99976	0,36238	0,99727	0,50076	0,99983	2,0174	0,02322
ECOL4764K	85853533	flgM	Anti-sigma factor for FliA (sigma (28))	Mobility (N)	0,34001	0,99976	0,69974	0,99727	0,58044	0,99983	1,97572	0,0005
ECOL4764K	85853534	flgN	Flagellar biosynthesis protein FlgN	Mobility (N)	−0,7733	0,99976	0,781	0,99727	0,90817	0,888	1,786	0,01351
ECOL4764K	85854634	crfC	Clamp-binding sister replication fork colocalization protein	Mobility/Biofilm (S)	1,70975	0,07724	1,95494	0,00099	2,21853	0,0002	4,27686	4,6E-07
ECOL4764K	85851287	pdeH	c-di-GMP phosphodiesterase PdeH	Signal transduction/ Biofilm (T)	1,46386	0,99976	1,66924	0,00446	1,71645	0,00094	3,34377	9,2E-09
ECOL4764K	85855159	aer	Aerotaxis sensor receptor, flavoprotein	Signal transduction (T)	0,77505	0,99976	0,55373	0,99727	0,57299	0,99983	2,01637	7,1E-08
ECOL4764K	85853407	ariR	Regulator of acid resistance, influenced by indole	Stress response (K)	−1,4935	0,99976	2,80049	0,04361	1,93625	0,08163	0,09459	0,99982
ECOL4764K	85854675	soxS	DNA-binding transcriptional dual regulator SoxS	Stress response (K)	0,87424	0,99976	2,21651	0,0026	2,98162	2E-08	0,28149	0,99982
ECOL4764K	85853493	bhsA	DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA	Stress response (M)	1,59777	0,29059	2,42131	0,00119	2,25489	2,7E-06	0,96289	0,99982
ECOL4764K	85855319	yhcN	DUF1471 domain-containing stress-induced protein YhcN	Stress response (S)	1,87275	0,07207	3,39818	0,00145	2,98628	0,00046	1,27996	0,99982
ECOL4764K	85851256	cspA	Cold shock protein CspA	Transcription (K)	1,12139	0,61924	1,56845	0,00214	2,01672	8,8E-06	1,01535	0,99982
ECOL4764K	85853716	infA	Translation initiation factor IF-1	Translation (J)	1,31764	0,30382	1,39097	0,02694	1,1611	0,16529	0,66463	0,99982
p4764_IncY.1	71940636		Phage protein	Phage-related gene	3,14456	0,0015	2,18085	0,00086	2,52625	0,00024	0,96609	0,99982
ECOL4764K	85854613	ghoT	Toxin of the GhoTS toxin-antitoxin system	Virulence (S)	0,83692	0,99976	1,12523	0,57857	1,84114	0,01536	1,14237	0,99982
ECOL4764K	85853786		AAA family ATPase		1,1885	0,64644	1,39583	0,06825	1,42295	0,03606	0,93341	0,99982
ECOL4764K	85853146	ydcI	Putative DNA-binding transcriptional repressor YdcI	Transcription (K)	−2,6947	0,01855	−1,0757	0,99727	−1,2121	0,57142	−0,9326	0,99982
ECOL4764K	85852863	lpp	Murein lipoprotein	Stress response (M)	−1,7995	0,26242	−3,3785	0,00014	−2,1319	0,27055	−2,8267	0,00396
ECOL4764K	85854468	fimA	Type 1 fimbriae major subunit	Adherence, virulence (NU)	−0,1746	0,99976	−1,3709	0,02694	−1,2625	0,04858	−1,1741	0,05009
ECOL4764K	85853794		Conserved protein of unknown function	Function unknown (S)	−2,6511	0,99976	−3,0843	0,03081	−2,7848	0,03065	−1,0916	0,99982
ECOL4764K	85854469		Conserved protein of unknown function	Function unknown (S)	−0,884	0,99976	−1,593	0,02238	−1,3599	0,05618	−1,0845	0,99982
ECOL4764K	85855200	cyuP	Putative D/L-serine transporter	Metabolism (E)	−2,4647	0,00398	−0,4576	0,99727	−0,0101	0,99983	0,09587	0,99982
ECOL4764K	85855214	garP	Galactarate/glucarate/glycerate transporter GarP	Metabolism (P)	−3,286	0,99976	−3,2159	0,03322	−2,191	0,40415	−1,2117	0,99982
ECOL4764K	85853531	flgB	Flagellar basal-body rod protein FlgB	Mobility (N)	−2,4376	0,01135	0,29403	0,99727	−0,0528	0,99983	1,05304	0,99982
ECOL4764K	85853758		Phage tail assembly protein	Phage-related gene	−5,9563	0,19907	−2,0276	0,05361	−2,0384	0,01677	−0,6334	0,99982
ECOL4764K	85853759		Major tail tube protein	Phage-related gene	−3,1385	0,02476	−3,3181	7,1E-05	−3,3456	1,4E-05	−0,7553	0,99982
ECOL4764K	85853760		Phage tail protein	Phage-related gene	−3,3751	0,01825	−3,3118	0,0003	−3,1419	0,00019	−0,615	0,99982
ECOL4764K	85853767		Baseplate assembly protein J	Phage-related gene	−2,738	0,64644	−2,4369	0,01225	−2,0464	0,01131	−0,4411	0,99982
ECOL4764K	85853769		Baseplate assembly protein V	Phage-related gene	−5,2672	0,40761	−1,9515	0,03139	−1,7238	0,05644	−0,4465	0,99982
ECOL4764K	85853774		Putative regulatory protein	Phage-related gene	−4,5905	0,73682	−2,4347	0,08358	−2,9586	0,00028	−0,7132	0,99982
ECOL4764K	85853775		Putative membrane protein	Phage-related gene	−5,7573	0,28603	−3,6302	0,00097	−3,3555	0,00137	−1,1559	0,99982
ECOL4764K	85853776		Prophage lysozyme ; Phage lysin	Phage-related gene	−4,9729	0,64535	−3,7054	0,00406	−3,1939	0,00726	−0,5838	0,99982
ECOL4764K	85853779		Phage head completion-stabilization protein	Phage-related gene	−5,7646	0,27944	−3,3571	0,00598	−3,2539	0,00252	−0,8388	0,99982
ECOL4764K	85853780		Phage terminase, endonuclease subunit	Phage-related gene	−6,0071	0,22056	−4,1881	0,00013	−4,1537	4E-05	−0,8143	0,99982
ECOL4764K	85853781		Phage major capsid protein, P2 family	Phage related gene	−4,9297	0,00621	−4,0468	4,2E-05	−4,3081	7,3E-07	−0,8018	0,99982
ECOL4764K	85853782		Phage capsid scaffolding protein	Phage-related gene	−3,2044	0,09625	−3,8346	6,9E-05	−3,9739	2E-05	−0,7085	0,99982

^{^a}

Boxes in gray color indicate genes that were statistically significantly different compared to UB12-RC (positive value = up-regulated; negative value = down-regulated) with p _adj <0.05 (dark gray) and with p _adj <0.1 (light gray); log2FC indicates the log₂ (fold-change), p _adj indicates the adjusted P-value

^{^b}

Gene Ontology terms are according to the BioCys Genome Database collection and eggNOG-mapper v2.