Table A1.

The most up- and downregulated host genes. The following genes of the wild type or dksA mutant hosts were found to be the most up- or downregulated hosts genes upon phage infection (regardless the time points). Double plus (++) represents host genes listed as the top ten most regulated at each time-point (the same as shown in Figure 3C or Figure 3D). One plus (+) indicates the host genes that were up- or downregulated, but their expression was lower than the top ten (therefore they were not shown in Figure 3). Minus (−) indicates that a gene was neither up- nor downregulated in the host. Arrows (↓↑) indicate the direction of regulation.

↓↑ Reg.	WT	dksA	Gene	Function
↓	++	++	cpxP	periplasmic adaptor protein
↓	++	++	cspA	RNA chaperone and antiterminator, cold-inducible
↓	++	++	cspB	Qin prophage; cold shock protein
↓	++	++	cspG	cold shock protein homolog
↓	++	++	lpxP	palmitoleoyl-acyl carrier protein
↓	++	++	mdtI	multidrug efflux system transporter
↓	++	++	mdtJ	multidrug efflux system transporter
↓	++	++	nepI	putative transporter
↓	++	++	yncD	putative iron outer membrane transporter
↓	++	+	cspF	Qin prophage, cold shock protein
↓	++	+	dtpA	dipeptide / tripeptide permease A
↓	++	−	hisD	bifunctional histidinal/histidinol dehydrogenase
↓	++	−	hisG	ATP phosphoribosyltransfer-ase
↓	++	−	kdpA	potassium translocating ATPase
↓	++	−	yccA	modu-lator of FtsH protease, inner membrane protein
↓	++	−	ydjN	putative transporter
↓	++	−	ydjO	uncharacterized protein
↓	++	−	ygbE	DUF3561 family inner membrane protein
↓	+	++	bluF	anti-repressor for YcgE
↓	+	++	mcbR	biofilm gene transcriptional regulator
↓	+	++	ylaB	put. membrane cyclic-diGMP phosphodiesterase
↓	−	++	cyoA	cyto-chrome o ubiquinol oxidase subunit II
↓	−	++	pdhR	pyruvate dehydrogenase complex repressor
↓	−	++	rhlE	ATP-dependent RNA helicase
↓	−	++	xseA	exonuclease VII
↓	−	++	ydcX	DUF2566 family protein
↓	−	++	yjcB	putative inner membrane protein
↑	−	++	cdd	cytidine/deoxycytidine deaminase
↑	++	+	fxsA	suppressor of F exclusion of phage T7
↑	++	+	ibpA	heat shock chaperone
↑	++	+	ibpB	heat shock chaperone
↑	++	−	insI1	IS30 transposase
↑	++	−	ogrK	orphan Ogr protein, positive regulator of P2 growth
↑	++	++	pgaA	biofilm adhesin polysaccharide PGA secretin
↑	++	+	pgaB	outer membrane export lipoprotein
↑	++	+	phoU	negative regulator of PhoR/PhoB two-component regulator
↑	++	+	pstA	phosphate ABC transporter permease
↑	++	+	pstS	phosphate ABC transporter periplasmic binding protein
↑	++	+	recA	DNA recombination and repair protein
↑	++	−	sra	stationary-phase-induced ribosome-associated protein
↑	++	+	uspG	universal stress protein UP12
↑	++	+	ybeL	DUF1451 family protein
↑	++	−	ycaC	putative isochorismatase family hydrolase
↑	++	+	ycjX	DUF463 family protein, puatative P-loop NTPase
↑	++	++	yjiY	putative transporter
↑	++	+	hdhA	7-alpha-hydroxysteroid dehydrogenase, NAD-dependent
↑	−	++	cysA	sulfate/thiosulfate transporter subunit
↑	−	++	cysC	adenosine 5’-phosphosulfate kinase
↑	−	++	cysD	sulfate adenylyltransferase, subunit 2
↑	−	++	cysH	phosphoadenosine phosphosulfate reductase
↑	−	++	cysI	sulfite reductase, beta subunit, NAD(P)-binding
↑	−	++	cysJ	sulfite reductase, alpha subunit, flavoprotein
↑	−	++	cysN	sulfate adenylyltransferase, subunit 1
↑	−	++	cysW	sulfate/thiosulfate ABC transporter permease
↑	−	++	fruA	fused fructose-specific PTS enzymes
↑	−	++	gatY	D-tagatose 1,6-bisphosphate aldolase 2, catalytic subunit
↑	−	++	gatZ	D-tagatose 1,6-bisphosphate aldolase 2, subunit
↑	−	++	gntP	fructuronate transporter
↑	−	++	malP	maltodextrin phosphorylase
↑	−	++	udp	uridine phosphorylase
↑	−	++	yeeE	UPF0394 family inner membrane protein
↑	−	++	yhaO	putative transporter