TABLE 3.

E. coli genes repressed more than threefold (P < 0.05) in an LB glu biofilm after 15 h at 37°C upon deleting ycfR

Group and gene	b no.a	Description	Expression ratio
tRNA
thrT	b3979	tRNA	−3.0
valX	b2402	tRNA	−3.2
valZ	b0746	tRNA	−3.0
Regulator
cspB	b1557	CspA family of cold shock protein	−5.7
cspG	b0990	Homolog of Salmonella cold shock protein	−3.0
lrhA	b2289	NADH dehydrogenase transcriptional regulator, LysR family	−3.2
marA	b1531	Regulator, drug/analog sensitivity	−3.0
putA	b1014	Bifunctional enzyme, as well as a transcriptional repressor of the put (proline utilization) regulon	−4.0
Transport and metabolism
atpB	b3738	Membrane-bound ATP synthase, F0 sector, subunit A	−3.5
atpE	b3737	Membrane-bound ATP synthase, F0 sector, subunit C	−3.0
atpF	b3736	ATP synthase, F0 complex, subunit B	−3.0
atpH	b3735	Membrane-bound ATP synthase, F1 sector, delta subunit	−3.2
feoA	b3408	Ferrous iron transport protein A	−3.2
gatA	b2094	GatA, subunit of EIIGat, galactitol PTS permease	−3.0
gatB	b2093	Transport, transport of small molecules: carbohydrates, organic acids, alcohols	−4.9
gatC	b2092	Transport, transport of small molecules: carbohydrates, organic acids, alcohols	−3.7
gatD	b2091	Enzyme, degradation of small molecules: carbon compounds	−4.0
nmpC	b0553	Outer membrane porin	−6.5
putP	b1015	Sodium/proline symporter responsible for the uptake of proline	−4.3
rbsD	b3748	d-Ribose high-affinity transport system; membrane-associated protein	−3.5
rbsA	b3749	ATP-binding component of d-ribose high-affinity transport system	−3.5
rbsC	b3750	d-Ribose high-affinity transport system	−3.5
sdaC	b2796	Probable serine transporter	−4.0
ompW	b1256	Outer membrane protein W; colicin S4 receptor; putative transport protein	−6.0
Metabolism
tnaA	b3708	Tryptophanase	−4.6
tnaL (tnaC)	b3707	Tryptophanase leader peptide	−4.9
yfiD	b2579	Putative formate acetyltransferase	−4.3
Unknown function
yeeI	b1976	Conserved hypothetical protein	−3.2

^ab no., a unique numeric identifier assigned to each E. coli gene.