TABLE 1 .

Cellular transcript abundances of selected genes significantly upregulated or downregulated under different nutrient regimes^a

No. of transcripts per 1,000 cells				Gene description	Locus	SD; significance
Deplete	Replete	Vitamin	DOM
17,897	10	10	8	Conserved hypothetical protein	NB46_00251	166/3/3/2; +++, −nn, −nn, −nn
3,093	3	3	3	Nitrogen regulatory protein PII	NB46_00250	86/1/1/1; +++, −nn, −nn, −nn
4,952	18	19	23	Ammonium transporter	NB46_00249	1,402/3/4/2; +++, −nn, −nn, −nn
32	2	1	1	Hypothetical protein KB13_177	NB46_00540	19/2/1/1; +++, −nn, −nn, −nn
425	35	69	83	Ammonium transporter	NB46_01065	119/2/14/8; +++, −nn, −nn, −nn
2,413	2,058	1,899	1,653	Glutamine synthetase, type I	NB46_00305	651/287/315/162; +++, −nn, −nn, −nn
1,228	236	379	370	Glycosyltransferase involved in cell wall biogenesis	NB46_00223	244/41/36/42; +++, −nn, −nn, −nn
869	177	184	173	Nitrogen regulation protein NtrB	NB46_00304	70/20/27/30; +++, −nn, −nn, −nn
2,826	565	1,162	936	IMP dehydrogenase	NB46_01283	792/108/135/90; +++, −nn, −nn, −nn
1,277	319	558	415	GMP synthase	NB46_01284	152/16/20/38; +++, −−n, −+n, −nn
88	994	446	175	Chaperone protein DnaJ	NB46_00532	6/473/30/3; −nn, +n+, nnn, n−n
69	889	363	165	Cochaperone GrpE	NB46_00534	8/496/73/14; −nn, +n+, nnn, n−n
127	2,066	1,064	493	Chaperone protein HtpG	NB46_00999	12/673/182/38; −−n, +++, ++n, n−n
372	4,704	2,003	944	Chaperone protein DnaK	NB46_00533	29/829/313/71; —n, +++, +−+, n−−
563	2,833	946	547	Chaperonin GroS	NB46_01193	43/543/208/15; −nn, +++, n−n, n−n
1,240	6,068	2,213	1,305	Chaperonin GroL	NB46_01192	167/681/325/55; —n, +++, −+−, n−−
570	750	718	560	Phosphate transport system regulatory PhoU	NB46_00097	75/34/32/50; —n, +n+, +n+, n−−
76	109	163	183	Phosphate-selective porins O and P	NB46_00625	28/34/22/32; n−−, nnn, +nn, +nn
40	83	119	162	Phosphate ABC transporter, periplasmic P-binding	NB46_00628	7/8/14/19; −−−, +−−, ++−, +++
154	240	453	439	Phosphate ABC transporter, permease PstC	NB46_00629	12/30/12/59; −−−, +−−, ++n, ++n
95	210	531	493	Phosphate ABC transporter, permease PstA	NB46_00630	9/29/20/49; −−−, +−−, ++n, ++n
94	280	457	361	Phosphate ABC transporter, ATP-binding	NB46_00631	20/52/32/16; −−−, +−−, +++, ++−
78	183	202	176	Phosphate regulon sensor protein	NB46_01228	8/99/6/10; nnn, nnn, nnn, nnn
134	264	1,213	989	PhnP protein	NB46_00720	8/53/78/99; −−−, +−−, +++, ++−
308	644	298	244	Fe-S protein assembly chaperone HscA	NB46_00974	42/268/9/24; nnn, nn+, nnn, n−n
109	155	87	88	Fe-S protein assembly cochaperone HscB	NB46_00975	15/45/13/7; nnn, nnn, nnn, nnn
170	350	163	230	Iron-sulfur cluster assembly protein IscA	NB46_00976	16/26/27/30; −n−, +++, n−−, −+−
134	5,304	574	309	TonB-dependent siderophore receptor	NB46_01062	8/1,302/38/44; −nn, +++, n−n, n−n
289	1,148	301	964	Putative TonB-dependent receptor	NB46_00103	15/321/22/71; −n, ++n, n−−, +n+
1,376	688	772	671	Ferritin and Dps	NB46_00108	79/103/47/48; +++, −nn, −nn, −nn
1,455	16,208	36,814	27,421	Bacteriorhodopsin	NB46_00176	121/1,449/4,097/3,176; −−−, +−−, +++, ++−
39	72	95	76	β-Carotene 15,15′-monooxygenase	NB46_00171	1/38/4/8; n−n, nnn, +nn, nnn
27	139	151	158	Lycopene cyclase protein	NB46_00172	2/67/19/15; −−−, +nn, +nn, +nn
22	106	93	113	Phytoene/squalene synthetase	NB46_00173	4/36/13/16; −−−, +nn, +nn, +nn
101	304	329	361	Phytoene desaturase	NB46_00174	21/129/34/43; −−−, +nn, +nn, +nn
147	522	630	673	Geranylgeranyl pyrophosphate synthase	NB46_00175	27/154/152/92; −−−, +nn, +nn, +nn
44	47	102	94	2-C-methyl-d-erythritol 2,4-cyclodiphosphate	NB46_01067	12/8/2/6; n−−, n−−, ++n, ++n
50	35	114	103	2-C-methyl-d-erythritol 4-phosphate transferase	NB46_01066	8/5/12/10; n−−, n−−, ++n, ++n
98	260	687	666	Peptidase PpqF	NB46_00526	24/58/38/72; −−−, +−−, ++n, ++n
180	379	863	750	Putative Xaa-Pro aminopeptidase 3	NB46_00896	14/111/75/74; −−−, +−−, ++n, ++n
66	234	715	683	Trypsin domain protein	NB46_01139	20/44/24/95; −−−, +−−, ++n, ++n
84	151	437	507	ABC-type dipeptide transport system, ATPase	NB46_00835	3/35/23/94; n−−, n−−, ++n, ++n
85	239	553	385	Peptide ABC transporter, permease protein	NB46_00784	10/127/21/34; −−−, +−−, +++, ++−
92	314	706	757	Sigma E regulatory protein, MucB/RseB, putative	NB46_00988	13/67/42/97; −−−, +−−, ++n, ++n
386	1,211	2,478	2,690	RNA polymerase sigma factor RpoE	NB46_00986	103/196/256/333; −−−, +−−, ++n, ++n
66	51	139	113	Sulfatase	NB46_00552	8/12/10/13; n−−, n−−, +++, ++−
121	230	648	511	Extracellular solute-binding protein, family 5	NB46_00783	5/83/46/71; n−−, n+−, +++, ++−
16	77	66	193	Hypothetical protein Neut_0862	NB46_00664	0/3/4/4; −−−, ++−, +−−, +++
12	30	28	70	FKBP-type peptidyl-prolyl cis-trans isomerase	NB46_01197	4/5/7/15; nn−, nn−, nn−, +++
101	269	420	1,055	Putative HpcH/HpaI aldolase/citrate lyase	NB46_00665	12/33/16/47; −−−, +−−, ++−, +++
104	341	487	1,045	Long-chain fatty acid–CoA ligase, putative	NB46_00666	17/93/21/76; −−−, +−−, ++−, +++

^aAbundances are the mean values of triplicates with the SDs in the far right column. Deplete, +MeOH −N −V; replete, +MeOH +N −V; vitamin, +MeOH +N +V; DOM, +DOM +N −V. Statistically significant upregulation (+) or downregulation (−) (ANOVA and t test; P < 0.05) by a treatment against the three other treatments is indicated in the far right column for each of the conditions (n, no significant difference) in the following order: deplete, replete, vitamin, and DOM. Table S2 in the supplemental material contains the cellular transcript abundances of all of the genes in NB0046.