. 2016 Dec 6;1(6):e00149-16. doi: 10.1128/mSystems.00149-16

TABLE 2 .

Genes upregulated during biofilm growth versus early log phase but downregulated during biofilm growth versus late log and stationary phases

M5005 locus^a	Gene	Log fold change^b,^c									Putative gene product or function^d	COG cluster(s)^e	Operon structure^f
		Early biofilm	Maturing biofilm	Late biofilm	Early biofilm	Maturing biofilm	Late biofilm	Early biofilm	Maturing biofilm	Late biofilm
		Versus early log phase			Versus late log phase			Versus early stationary phase
Spy0040	adhA	1.93	2.02	2.2	−2.73	−2.64	−2.46	−1.86	−1.77	−1.59	Alcohol dehydrogenase	R
Spy0118		1.4	1.33		−1.03	−1.09	−1.45	−1.47	−1.53	−1.89	LysR family transcriptional regulator	K
Spy0151	ulaD			1.69	−2.57	−2.46	−2.02	−1.88	−1.77	−1.33	3-Keto-l-gulonate-6-phosphate decarboxylase	G	A
Spy0152			1.55	1.86	−3.05	−2.89	−2.58	−2.03	−1.87	−1.56	Putative l-xylulose 5-phosphate 3-epimerase	G	A
Spy0153	araD			1.68	−3.89	−2.84	−2.35	−3.13	−2.08	−1.59	l-Ribulose-5-phosphate 4-epimerase	G	A
Spy0212		2.02	1.85	1.61	−1.96	−2.13	−2.38	−1.7	−1.86	−2.11	N-Acetylmannosamine-6-phosphate 2-epimerase	G	B
Spy0213		1.82	1.83	1.55	−2.07	−2.05	−2.34	−1.83	−1.82	−2.1	N-Acetylneuraminate-binding protein	G	B
Spy0214		1.08	1.08		−1.4	−1.41	−1.63	−1.34	−1.34	−1.57	N-Acetylneuraminate transport system permease	G
Spy0340	lctO	5.77	5.57	5.17	−2.6	−2.8	−3.2	−2.28	−2.47	−2.88	l-Lactate oxidase	C, I
Spy0341		4.37	4.72	4.2	−2.27	−1.93	−2.45	−2.7	−2.36	−2.88	Lactocepin	O
Spy0534		2.31	2.18	2.8	−1.63	−1.77	−1.14	−1.74	−1.87	−1.25	Acetoin reductase	I, Q
Spy0790	gabD	1.7	1.92	2.01	−1.34	−1.12	−1.04	−1.83	−1.61	−1.52	Succinate-semialdehyde dehydrogenase	C
Spy0834		4.06	3.77	3.47	−0.85	−1.14	−1.44	−0.83	−1.12	−1.42	Zn-dependent alcohol dehydrogenase	E
Spy0971		1.09	1.42	2.11	−1.74	−1.41	−0.72	−2.91	−2.58	−1.89	Gls24 family general stress protein	S	C
Spy0974		1.14	1.41	2.75	−2.26	−2	−0.66	−2.71	−2.45	−1.11	Small integral membrane protein	S	C
Spy0975		1.85	2.1	2.83	−1.68	−1.43		−2.22	−1.97	−1.24	Hypothetical protein		C
Spy1062	malA	1.65	1.69	2.63	−2.15	−2.11	−1.17	−2.53	−2.49	−1.55	Maltodextrose utilization protein	G	D
Spy1063	malD	2.59	2.5	2.16	−1.32	−1.41	−1.75	−1.37	−1.46	−1.79	Maltodextrin transport system permease protein	G	D
Spy1064	malC	3.04	2.85	2.27	−0.95	−1.13	−1.71	−1.25	−1.44	−2.01	Maltose transport system permease protein	G	D
Spy1065	amyA	2.62	2.52	2.79	−1.1	−1.2	−0.93	−1.73	−1.83	−1.56	Alpha-amylase	G	D
Spy1066	amyB	2.27	2.05	2.33	−1.51	−1.73	−1.44	−1.78	−2.01	−1.72	Cyclomaltodextrinase	G	D
Spy1067	malX	3	2.76	2.78	−1.32	−1.56	−1.54	−1.62	−1.85	−1.84	Maltose/maltodextrin-binding protein	G
Spy1093		3.09	2.98	2.63	−1.84	−1.95	−2.3	−1.69	−1.81	−2.15	Hypothetical protein	R
Spy1270	arcC	4.2	4.39	5.17	−3.65	−3.46	−2.68	−3.67	−3.48	−2.7	Carbamate kinase	E	E
Spy1271	arcT	5.42	5.42	5.7	−2.85	−2.85	−2.58	−2.66	−2.66	−2.39	Xaa-His dipeptidase	E	E
Spy1272	arcD	4.63	4.76	4.92	−3.53	−3.39	−3.24	−2.94	−2.8	−2.65	Arginine/ornithine antiporter	R	E
Spy1273	arcB	4.73	4.72	4.72	−3.6	−3.6	−3.61	−2.62	−2.63	−2.63	Ornithine carbamoyltransferase	E	F
Spy1274		4.82	4.92	6.04	−3.94	−3.84	−2.72	−3.32	−3.22	−2.1	Acetyltransferase	-	F
Spy1275	arcA	5.4	6.02	5.9	−3.54	−2.92	−3.05	−2.63	−2	−2.13	Arginine deiminase	E	F
Spy1314	hyl	1.12	1.35	1.17	−1.72	−1.5	−1.67	−1.7	−1.48	−1.65	Hyaluronoglucosaminidase	-
Spy1316		1.04	2.03	1.66	−1.72	−0.72	−1.09	−2.11	−1.12	−1.49	Hypothetical protein	S
Spy1376	tal	1.14	1.35	1.38	−1.96	−1.74	−1.71	−1.92	−1.7	−1.67	Putative translaldolase	G
Spy1395	lacD.1	3.34	3.58	3.45	−1.75	−1.5	−1.63	−1.55	−1.3	−1.43	Tagatose 1,6-diphosphate aldolase	G
Spy1396		3.37	3.8	4.18	−2.49	−2.07	−1.69	−2.4	−1.97	−1.6	Tagatose-6-phosphate kinase	-	G
Spy1397	lacB.1	3.21	3.48	4.08	−2.6	−2.32	−1.73	−2.22	−1.95	−1.36	Galactose-6-phosphate isomerase subunit LacB	G	G
Spy1398	lacA.1	3.56	3.84	4.16	−2.32	−2.04	−1.72	−2.14	−1.86	−1.54	Galactose-6-phosphate isomerase subunit LacA	G	G
Spy1399		4.39	4.46	4.47	−2.95	−2.89	−2.88	−2.51	−2.44	−2.43	PTS, galactose-specific IIC component	G	H
Spy1400		4.61	5.81	5.78	−3.16	−1.97	−2	−2.61		−1.44	PTS, galactose-specific IIB component	G	H
Spy1401		4.3	4.48	5.03	−3.34	−3.16	−2.6	−2.2	−2.02	−1.47	PTS, galactose-specific IIA component	G, T	H
Spy1632	lacG	1.62	2.67	2.2	−2.85	−1.81	−2.28	−2.03	−0.99	−1.46	6-Phospho-beta-galactosidase	G	I
Spy1633	lacE	2.69	3.99	3.08	−3.63	−2.33	−3.24	−2.52	−1.22	−2.13	PTS, lactose-specific IIBC component	G	I
Spy1634	lacF	3.54	4.8	4.1	−3.44	−2.17	−2.87	−2.44		−1.88	PTS, lactose-specific IIA component	G	I
Spy1635	lacD.2	3.99	5.45	4.37	−2.92	−1.45	−2.53	−1.99		−1.6	Tagatose 1,6-diphosphate aldolase	G	I
Spy1636	lacC.2	3.21	4.26	3.41	−3.19	−2.14	−3	−1.7		−1.51	Tagatose-6-phosphate kinase	G	I
Spy1637	lacB.2	4.1	5.17	3.54	−2.11	−1.03	−2.66	−1.05		−1.61	Galactose-6-phosphate isomerase subunit LacB	G	I
Spy1638	lacA.2	3.82	4.91	4.11	−2.51	−1.41	−2.21	−1.72		−1.42	Galactose-6-phosphate isomerase subunit LacA	G	I
Spy1744		1.93	2.28	2.41	−1.9	−1.56	−1.42	−1.52	−1.18	−1.04	PTS, cellobiose-specific IIC component	G
Spy1758		2.04	2.14	2.22	−1.29	−1.19	−1.11	−1.54	−1.44	−1.36	Dipeptidase B	E
Spy1769	ahpF	1.39	1.22	1.08	−0.9	−1.07	−1.21	−2.14	−2.31	−2.46	Peroxiredoxin reductase [NAD(P)H]	V
Spy1783	dexS	3.44	3.28	3.87	−1.51	−1.67	−1.08	−1.87	−2.04	−1.44	Trehalose-6-phosphate hydrolase	G	J
Spy1784		3.54	3.04	3.35	−1.65	−2.15	−1.83	−1.87	−2.37	−2.05	PTS, trehalose-specific IIBC component	G	J

Data represent genes that were upregulated in biofilm versus the early log phase and downregulated in biofilm versus the late log and stationary phases.

Numbers represent log₂ fold change between the biofilm and planktonic time points.

Missing numbers indicate that differential expression data were not statistically significant for the given comparison.

Gene descriptions derived from the NCBI and/or Uniprot database.

Letters refer to the functional categories of the assigned Cluster of Orthologous Group (COG) (http://www.ncbi.nlm.nih.gov/COG).

Identical letters indicate genes predicted to be in the same operon according to analysis by the program Rockhopper.