Table 2.

Most Strongly Downregulated FtsH3-Dependent and Fe-Independent Protein-Coding Genes, log₂FC ≤ −2

Functional Category	Gene Name(s)	TU No.	Protein Name(s)	log2FC = (FtsH3 − WT)
Pho regulon	sll0680–sll0684	TU2785	PstS1, PstC1, PstA1, PstB1, PstB1’	−4.2 to −2.2
	slr1247–slr1249	TU1428	PstS2, pstC2, PstA2	−3.9 to −2.3
	sll0654, sll0656	TU388	Alkaline phosphatase, NucH	−3.4 to −2.4
Translation (RP, EF)	sll1743–sll1746	TU931	RpL11, RpL1, RpL10, RpL12 RpL3, RpL4,	−3.2 to −2.1
	sll1799–sll1807	TU837	RpL23, RpL2, RpS19, RpL22, RpS3, RpL16, RpL29, Rps17, RpL14, RpL24	−2.8 to −2.1
	ssr0482	TU2205	RpS16	−2.7
	sll1096–sll1101	TU1986	RpS12, RpS7, elongation factor EF-TU, Rps10	−2.6 to −2.2
	ssr1398; ssr1399	TU298	RpL33; RpS18	−2.6; −2.3
	sll1816–sll1822,	TU833	RpS13; RpS11, Rps9	−2.4; −2.1
	sll1426;sll0767	TU2501	Rpl35; Rpl20	−2.2; −2.1
	slr0628	TU2793	RpS14	−2.2
	ssl1784	TU332	RpS15	−2.2
	ssl2233	TU865	RpS20	−2.1
	slr1678	TU2627	RpL21	−2.0
	slr1356	TU1129	RpS1 homolog A	−2.0
	sll1260	TU1778	RpS2	−2.0
	sll1261	TU1777	Elongation factor Ts, EF-Ts	−2.2
	slr0083	TU3046	ATP-dependent RNA helicase CrhR	−2.1
	ssl3177	TU1030	Uncharacterized protein Ssl3177	−2.0
Photosynthesis, energy	ssl0020	TU2593	Ferredoxin-1, PetF	−3.3
	sll0819	TU1727	PSI reaction center subunit III, PsaF	−2.1
	sll1317	TU1200	Apocytochrome f, PetA	−2.0
	ssl2615; sll1322	TU166	ATP synthases subunits AtpH; AtpI	−2.4; −2.3
Toxin-antitoxin systems	ssl2245, sll1130	TU1078	Ssl2245 antitoxin, Sll1130 toxin	−2.8; −2.7
Unknown proteins	slr0287	TU2207	Slr0287 protein	−2.6
	ssl2874	TU3563	UPF0296 protein Ssl2874	−2.4

Genes were considered FtsH3-dependent and Fe-independent when log₂ FC ≈ log₂FC_Fe ≥ 1. FCs between the wild type (WT) and FtsH3down mutant were calculated by subtracting the corresponding wild-type value. The P-values of all listed log₂FC were ≤0.05. All genes belonging to the same transcriptional unit (TU) are listed in one line, with the range in log₂FC values shown at the end. TUs were defined previously (Kopf et al., 2014). EF, elongation factor.