. 2020 May 18;117(21):11207–11216. doi: 10.1073/pnas.1919888117

Table 2.

Phage-resistant mutations isolated from the fluctuation experiment

Culture ^#	Isolate ID	U136B^R	tolC mutation^†	TET MIC (μg/mL)^‡	LPS mutation^†^,^§	CST MIC (ng/mL)^¶	Other genes with mutations^†^,^#
Controls
BW25113		−		2.0		250
tolC knockout		+	∆tolC732::kan	0.50		250
Phage-resistant mutants
1	RGB-036	+		4.00	rfaF, IS1E interruption, coding 162/1,047 nt	100
2	RGB-040	+	Q158* (CAA→TAA)	0.50		150
3	RGB-045	+	Δ1 bp, coding 1091/1482 nt	0.50		200
4	RGB-049	+		4.00	ΔghmA within 48-gene deletion^#	100	48-gene deletion; see SI Appendix, Table S4
5	RGB-058	+		2.00	rfaG, IS1E interruption coding 604/1125 nt	100	ydeM, C345F (TGC→TTC)
6	RGB-060	+		2.00	rfaP, E59* (GAG→TAG)	100
7	RGB-065	+		4.00	ΔghmA within 48-gene deletion^#	100	48-gene deletion; see SI Appendix, Table S4
8	RGB-071	+	IS5-interupted, coding 190/1482 nt	0.50		200
9	RGB-074	+		2.00	rfaP, IS1E interruption, coding 523/798 nt	150
10	RGB-079	+		4.00	rfaD, Y272N (TAT→AAT)	50
11	AB350	+	Δ6 bp at 396/1482 nt	0.50		250
12	AB351	+		4.00	ΔghmA within 48-gene deletion^#	100	48-gene deletion; see SI Appendix, Table S4
13	AB352	+	IS5-interupted, coding 190/1482 nt	0.50		250
14	AB353	+		4.00	rfaP, IS1E insertion, coding 322/798 nt	100
15	AB354	+		4.00	rfaP, Δ1 bp, coding 386/798 nt	100
16	AB355	+		4.00	rfaC, Δ10 bp, coding 582/960 nt	100
17	AB356	+		4.00	rfaF, IS1E interrupted coding 314/1,047 nt	100
18	AB357	+		4.00	rfaD, Δ1 bp, coding 585/933 nt	100
19	AB358	+	tolC IS5 insertion, coding (585/933 nt)	0.50		250
20	AB359	+		4.00	rfaF, IS1E interruption, coding 162/1,047 nt	150

^{^†}

A “Δ” indicates deletion of indicated base pairs or gene. An asterisk indicates a point mutation resulting in a stop codon. Values in parentheses indicate either single substitutions or the location of either a stop codon or IS element insertion within coding sequences. Underlined bases indicate single substitutions; nt, indicates nucleotide.

^{^‡}

Tetracycline (TET) concentrations tested were 0.125, 0.25, 0.5, 1.0, 2.0, and 4.0 μg/mL, so the discrete value listed may be greater than the actual MIC but not more than the next highest value tested. Values are the mode of four to five replicates tested for each mutant.

^{^§}

All rfa gene names are synonymous with the corresponding waa gene names used in the BW25113 annotation (e.g., waaP is equivalent to rfaP). Gene rfaD is synonymous with the hldD gene name used in the BW25113 annotation. We report mutations in the rfa form for readability.

^{^¶}

Colistin (CST) concentrations tested were 12.5, 25, 50, 100, 150, 200, 250, 300, 350, and 400 ng/mL, so the discrete value listed may be greater than the actual MIC but not more than the next highest value tested. Values are the mode of four to seven replicates tested for each mutant.

^{^#}

The 48-gene deletion included LPS synthesis gene gmhA (also called lpcA), which codes for a phosphoheptose isomerase involved in LPS synthesis (41–43). A full list of the 48 genes and their annotations is included in SI Appendix, Table S4. Gene ydeM putatively encodes a YdeN-specific sulfatase-maturating enzyme.