TABLE 2.

Changes in expression of genes under anaerobic-dark-DMSO conditions

Gene	Gene product	Change (n-fold) in gene expression in R. sphaeroides PrrA− PpsR− compared to PRRA2a	Change (n-fold) in gene expression in R. sphaeroides PrrA− PpsR− compared to wild typeb	Change (n-fold) in gene expression in R. sphaeroides PRRA2 compared to wild typec
Genes playing a role in PS development affected by prrA and/or ppsR mutation and located in the PGC
RSP0254	DxsA	26.29	2.69	−9.76
RSP0255	PufX	66.07	2.42	−27.26
RSP0256	PufM	112.64	2.52	−44.62
RSP0257	PufL	119.79	2.58	−46.4
RSP0258	PufA	47.5	3.72	−12.76
RSP0259	PufQ	134.47	3.93	−34.22
RSP0260d	BchZ	99.07	6.97	−14.22
RSP0261d	BchY	89.25	10.74	−8.31
RSP0262d	BchX	198.65	13.19	−15.06
RSP0263d	BchC	88.9	9.41	−9.45
RSP0264d	CrtF	13.23	2.96	NDe
RSP0265d	CrtE	14.34	ND	−12.28
RSP0266d	CrtD	7.86	2.62	−3
RSP0267d	CrtC	7.34	1.8	−4.07
RSP0269d	TspO	13.43	3.59	−3.74
RSP0270d	CrtB	18.3	4.3	−4.26
RSP0271d	CrtI	21.79	3.56	−6.12
RSP0272d	CrtA	38.85	2.02	−19.19
RSP0273	BchI	11.51	1.29	−8.89
RSP0274	BchD	2.8	ND	−3.18
RSP0276	IdI	12.52	3.1	−4.04
RSP0277d	BchP	17.35	2.86	−8.43
RSP0278d	RSP0278	21.33	2.83	−7.52
RSP0279d	BchG	19.33	2.3	−8.42
RSP0280d	BchJ	7.99	ND	−6.83
RSP0281d	BchE	19.34	1.57	−12.34
RSP0282	PpsR	−18.84	−16.94	ND
RSP0283d	PpaA	22.83	2.83	−8.07
RSP0284d	BchF	95.93	9.58	−10.01
RSP0285d	BchN	30.07	3.88	−8.91
RSP0286d	BchB	44.49	4.3	−10.36
RSP0287	BchH	63.84	3.88	−16.47
RSP0288	BchL	74.58	4.22	−17.67
RSP0289	BchM	53.46	6.63	−8.06
RSP0290	RSP0290	39.17	1.97	−19.9
RSP0291	PuhA	40.86	2.06	−19.8
RSP0292	Hypothetical protein	44.99	2.78	−16.18
RSP0293	Hypothetical protein	43.39	4.87	−8.91
RSP0294	Hypothetical protein	33.55	8.32	−4.03
RSP0295	Hypothetical protein	24.87	5.7	−4.37
RSP0296	CycA	19.44	5.57	−3.49
RSP0314d	Puc1B	404.47	2.77	−145.08
RSP0315d	Puc1C	+17.82	1.77	−10.05
Genes playing a role in PS development affected by prrA and/or ppsR mutation and located outside the PGC
RSP0692	RdxB	1.98	ND	−2.31
RSP0693	CcoP	4.36	1.82	−2.4
RSP0694	CcoQ	5	1.8	−2.78
RSP0695	CcoO	5.32	1.83	−2.91
RSP0696	CcoN	5.28	1.83	−2.89
RSP0679d	HemC	1.87	1.81	ND
RSP0680d	HemE	4.4	2.4	−1.84
RSP1556d	Puc2B	24.83	−1.79	−44.33
RSP1557d	Puc2A	14.06	−3.49	−49.02
RSP1518	PrrA	ND	−92.07	−282.22
RSP1518 copy 1	PrrA	ND	−28.42	−258.16
RSP1518 copy 2	PrrA	ND	−45.06	−236.18
RSP1518 copy 3	PrrA	ND	−47.67	−164.02
RSP1518 copy 4	PrrA	ND	−89.49	−275.86
Genes affected by prrA and/or ppsR mutation and located outside the PGC
RSP0381	PhaP	11.68	3.1	−3.77
RSP0382	PhaC	2.32	ND	−2.39
RSP0383	PhaZ	2.47	ND	−2.15
RSP2122	Putative dimethylamine corrinoid protein	27.21	19.05	ND
RSP2768	MetH homologue	4.47	3.15	ND
RSP2769	MetF homologue	17.36	10.49	ND
RSP2770	Conserved hypothetical protein	21.7	8.56	ND
RSP3241	Partial transcriptional regulatory protein with C-terminal homology to OmpR	2.5	1.64	ND
RSP3242	Putative trypsin-like serine protease	23.31	25.92	ND

^aData were obtained from references 11 and 21.

^bData were obtained from references 21 and 28.

^cData were obtained from references 11, 21, and 28.

^dGene known or predicted to be directly regulated by PpsR. The pufBA and puc1BA genes are represented by one probe set on the GeneChip (42).

^eND, not detectable.