TABLE 2.

Genes identified to affect the tolerance of P. putida towards F⁻ stress ^a

Gene	Locus	Insertions	Log2(FC)	p‐value	Description	References	Comments
rarA	PP_4002	3	−4.14	2.13 × 10−7	Recombination factor protein RarA	Reva et al. (2006)	Part of the PP_3999‐PP_4004 operon together with crcB; relevant under acid (HCl) stress (pH = 4.5).
			−3.46	0.0047
			−2.33	0.0077
crcB	PP_4001	1	−2.79	0.0151	Fluoride channel	—	Fluoride‐specific exporter
prtR	PP_2889	7	−2.63	8.16 × 10−5	Transmembrane anti‐σ factor PrtR	Burger et al. (2000); Llamas et al. (2014); Song et al. (2014); Calero et al. (2018)	Forms an operon with the stationary‐phase σ factor PrtI gene (PP_2888). PrtR controls the formation of external proteases and siderophores in P. fluorescens, as well as temperature‐dependent lipases and proteases. Also involved in tolerance towards p‐coumaric acid
			−2.91	0.0111
			−2.45	7.21 × 10−5
			−2.14	0.0044
			−3.00	4.79 × 10−5
			−3.57	0.0002
			−2.60	0.0231
lapA	PP_0168	4	−2.50	0.0009	Putative surface adhesion protein	Reva et al. (2006)	Involved in biofilm formation; plays a role in tolerance towards urea
			−2.77	0.0392
			−2.21	6.22 × 10−8
			−2.18	0.0006
	PP_1779	2	−4.13	0.0046	Lipopolysaccharide ABC export system, ATP‐binding protein	Cuthbertson et al. (2010)	Mediates polysaccharides export for the formation of glycosylated macromolecules
			−4.57	0.0009
lapD	PP_0165	1	−2.21	0.0471	Transmembrane protein	—	Bis‐(3′,5′)‐cyclic dimeric GMP‐binding protein; involved in surface attachment
fleQ	PP_4373	1	−2.32	0.0341	Transcriptional regulator	—	Bis‐(3′,5′)‐cyclic dimeric GMP‐responsive transcriptional regulator
flhA	PP_4344	1	−2.59	0.0121	Flagellar biosynthesis protein FlhA	—	Flagella assembly
yijP	PP_2579	1	−2.33	0.0018	Phosphoethanolamine transferase CptA	Mumm et al. (2016)	Involved in biosynthesis and modification of lipopolysaccharides. Subjected to regulation by ColRS
	PP_2525	1	−2.03	4.68 × 10−7	Hypothetical protein	—	ATP‐binding protein, ATPase; 59% identity with SufC, a Fe‐S assembly ATPase, in Shewanella oneidensis MR‐1
metH	PP_2375	3	−2.21	0.0221	B12‐dependent methionine synthase	Domínguez‐Cuevas et al. (2006); Molina‐Henares et al. (2010)	Last step of l‐methionine biosynthesis; upregulated in presence of toluene and o‐xylene in P. putida KT2440
			−2.07	0.0431
			−2.08	0.1211
curA	PP_2476	1	−2.48	0.0044	NADPH‐dependent curcumin/dihydrocurcumin reductase	Follonier et al. (2011)	Zinc‐containing alcohol dehydrogenase. Overexpressed when cells are stressed in pressurized cultures
ctpL	PP_0562	1	−2.08	0.0191	Methyl‐accepting chemotaxis sensory transducer	—	Chemoreceptor for 4‐chloroaniline and catechol in P. aeruginosa
	PP_1684	1	−2.17	0.0111	Major facilitator superfamily transporter	Follonier et al. (2013); Molina‐Santiago et al. (2016)	Efflux pump. Overexpressed when cells are stressed in pressurized cultures. Differentially expressed in toluene‐containing cultures
	PP_2411	1	−2.08	0.027	Major facilitator family transporter	—	Unknown
	PP_1922	1	−2.51	0.0022	Hypothetical protein	—	DUF2726 domain‐containing protein (unknown)
	PP_2857	1	−2.48	0.0028	Hypothetical protein	—	Orthologue to P. fluorescens F113 PSF113_2684 and P. putida H8234 L483_12195 (autotransporter adhesin)
	PP_1882	1	−2.19	0.014	Hypothetical protein	—	Predicted to be a membrane protein; contains a YD (tyrosine‐aspartate) repeat. Similar to Rhs proteins
	PP_2298	1	−2.63	0.014	Hypothetical protein	—	Unknown
	PP_2398	1	−2.08	0.017	Hypothetical protein	—	Small peptide
	PP_1631	1	−2.27	0.020	Hypothetical protein	Seo and Kim (2018)	Putative decarboxylase. Similar to LOG family proteins, which are not very well known in prokaryotic organisms but apparently related to microbe–plant interactions
	PP_0925	1	−2.14	0.024	Hypothetical protein	—	Orthologue to an acyl‐CoA dehydrogenase present in other Pseudomonas species

^a FC, fold change; LOG proteins, lonely guy proteins; CoA, coenzyme A. The references in the table indicate reports of the corresponding gene or function in either P. putida KT2440 or related species.