TABLE 3.

Genes repressed more than fourfold in LB glu medium biofilms upon deleting ydgG

Group and gene	b no.	Expression ratio	Description	Protein size (aa)
Synthesis and metabolism
gadA	b3517	−13	Glutamate decarboxylase isozyme	466
gadB	b1493	−10.6	Glutamate decarboxylase isozyme	466
aceA	b4015	−5.7	Isocitrate lyase	434
fadB	b3846	−4.9	Four-enzyme protein: 3-hydroxyacyl-CoAa dehydrogenase, 3-hydroxybutyryl-CoA epimerase, delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase, enoyl-CoA hydratase	729
nrdH	b2673	−4.6	Glutaredoxin-like protein; hydrogen donor	81
thrL	b0001	−4.3	thr operon leader peptide	21
Metabolism and transport
fadL	b2344	−6.1	Transport of long-chain fatty acids; sensitivity to phage T2	448
Transport
gadC (xasA)	b1492	−11.3	Acid sensitivity protein, putative transporter	512
dppA	b3544	−7	Dipeptide transport protein	535
DNA related
priB	b4201	−4.9	Primosomal replication protein N	104
tsf	b0170	−4	Protein chain clongation factor EF-Ts	283
RNA related
rpoE	b2573	−4.9	RNA polymerase, sigma-E factor; heat shock and oxidative stress	191
leuT	b3798	−4.6	Leucine tRNA1, duplicate with leuVPO	87
leuV	b4368	−4.6	Leucine tRNA1, tandemly triplicate leuVPQ, duplicate with leuT	88
thrT	b3979	−4.6	Threonine tRNA3	76
leuP	b4369	−4	Leucine tRNA1, tandemly triplicate leuVPO, duplicate with leuT	87
leuQ	b4370	−4	Leucine tRNA1, tandemly triplicate, duplicate with leuT	87
Ribosome components
rplC	b3320	−8.6	50S ribosomal subunit protein L3	209
rplB	b3317	−8	50S ribosomal subunit protein L2	273
rplW	b3318	−7.5	50S ribosomal subunit protein L23	100
rpsJ	b3321	−7.5	30S ribosomal subunit protein S10	103
rpsS	b3316	−7.5	30S ribosomal subunit protein S19	92
rplD	b3319	−6.1	50S ribosomal subunit protein L4; regulates expression of S10 operon	201
rplV	b3315	−6.1	50S ribosomal subunit protein L22	110
rpsC	b3314	−6.1	30S ribosomal subunit protein S3	233
rpmB	b3637	−5.3	50S ribosomal subunit protein L28	78
rpsB	b0169	−5.3	30S ribosomal subunit protein S2	241
rpsF	b4200	−5.3	30S ribosomal subunit protein S6	131
rplU	b3186	−4.9	50S ribosomal subunit protein L21	103
rpsR	b4202	−4.9	30S ribosomal subunit protein S18	75
rpmG	b3636	−4.6	50S ribosomal subunit protein L33	55
rplK	b3983	−4.3	50S ribosomal subunit protein L11	142
rplP	b3313	−4	50S ribosomal subunit protein L16	136
rpmC	b3312	−4	50S ribosomal subunit protein L29	63
Cell processes
gadE (yhiE)	b3512	−12.1	ORF, hypothetical protein; related to resistance at low pH	175
hdeA	b3510	−9.8	ORF, hypothetical protein; acid resistance protein, possible chaperone, subunit of HdeA dimer, inactive form of acid resistance protein	110
ORFs with unknown function
hdeB	b3509	−9.2	ORF, hypothetical protein; 10K-L protein, related to acid resistance protein of Shigella flexneri	112
hdeD	b3511	−9.8	ORF, hypothetical protein; protein involved in acid resistance	190
ybaW	b0443	−5.3	ORF, hypothetical protein	132
yciE	b1257	−4	ORF, hypothetical protein	168
ymgB	b1166	−4.3	ORF, hypothetical protein	88
ymgC	b1167	−4.3	ORF, hypothetical protein	82
yodC	b1957	−4	ORF, hypothetical protein	60

^aCoA, coenzyme A.