TABLE 2.

Regulation and function of quantified proteins involved in respiration.

Protein	Function	Regulation	-LOG(P-value)	Difference
CccA	Cytochrome c550	↓	1.29	–0.25
CccB	Cytochrome c551	=	0.38	–0.07
CtaC	Cytochrome-c oxidase (subunit II)	↓	4.07	–0.76
CtaD	Cytochrome-c oxidase (subunit I)	↓	3.52	–0.77
CtaE	Cytochrome-c oxidase (subunit III)	↓	3.07	–0.65
CtaF	Cytochrome-c oxidase (subunit IV)	↓	3.24	–0.84
CtaG	Formation of functional cytochrome C-oxidase (caa3)	↓	3.04	–0.71
CydA	Cytochrome bd ubiquinol oxidase (subunit I)	↓	3.28	–0.87
CydB	Cytochrome bd ubiquinol oxidase (subunit II)	↓	3.52	–0.82
CydC	ABC transporter required for expression of cytochrome bd	↓	3.81	–0.97
CydD	ABC transporter required for expression of cytochrome bd	↓	3.18	–0.71
NarG	Nitrate reductase (α subunit)	OFF
NarH	Nitrate reductase (β subunit)	OFF
NarI	Nitrate reductase (γ subunit)	OFF
NarK	Nitrite extrusion protein	OFF
Ndh	NADH dehydrogenase	↑	2.31	0.31
QcrA	Rieske factor, menaquinol:cytochrome c oxidoreductase (iron-sulfur subunit)	↓	2.97	–0.49
QcrB	Menaquinol:cytochrome c oxidoreductase (cytochrome b subunit)	↓	2.23	–0.27
QcrC	Menaquinol:cytochrome c oxidoreductase (cytochrome b/c subunit)	↓	2.72	–0.29
QoxA	Cytochrome aa3 quinol oxidase (subunit II)	=	0.62	–0.05
QoxB	Cytochrome aa3 quinol oxidase (subunit I)	=	0.29	–0.05
QoxD	Cytochrome aa3 quinol oxidase (subunit IV)	=	0.57	0.17
QoxD	Cytochrome aa3 quinol oxidase (subunit III)	=	0.04	0.03
ResA	Cytochrome c biogenesis	↓	3.42	–0.26
ResB	Cytochrome c biogenesis	↓	2.90	–0.25
ResC	Cytochrome c biogenesis	↓	1.83	–0.25
Sco	Maturation of cytochrome c oxidase caa3	↓	2.77	–0.37
YojN	Unknown	↑	3.39	0.39

Absolute amounts for all quantified proteins and regulation of significantly changed abundances can be found in Supplementary Tables S5, S6, respectively.