The Escherichia coli GcvB sRNA Uses Genetic Redundancy to Control cycA Expression

Table 1

Strains, plasmids, and phage.

Strains*, plasmids, and phage	Relevant genotype	Source or reference
Strains
GS162	WT	This lab
GS1144	ΔgcvB	[3]
GS1148	Δhfq	[13]
Plasmids
pGS341	Single-copy vector + WT gcvA	[17]
pGS594	Single-copy vector + WT gcvB	This lab
pGS596	pGS594 with a -TGT- to -CCC- change of bps +71 to +73 in gcvB (p𝑔𝑐𝑣𝐵^+71CCC)**	[3]
pGS602	pGS594 with a -TGT- to -AAA- change of bps +76 to +78 in gcvB (p𝑔𝑐𝑣𝐵^+76AAA)	[3]
pGS629	pGS594 with a -TGTT- to -CCCA- change of bps +79 to +82 in gcvB (p𝑔𝑐𝑣𝐵^+79CCCA)	[4]
pGS634	pGS594 with a -TG- to -CA- change of bps +142 and +143 and a -TG- to -CC- change of bps +159 and +160 in gcvB (p𝑔𝑐𝑣𝐵^+142CA+159CC)	[2]
pGS642	Single-copy vector + 𝑔𝑐𝑣𝐵^t1↑ allele (see Figure 2 for bp changes) (p𝑔𝑐𝑣𝐵^t1↑)	This study
pGS644	pGS634 with a -T- to -C- change of bp +79 in gcvB (p𝑔𝑐𝑣𝐵^+142CA+159CC+79C)	This study
pGS645	pGS634 with a -G- to -A- change of bp +80 in gcvB (p𝑔𝑐𝑣𝐵^+142CA+159CC+80A)	This study
pGS647	pGS642 with -TGT- to -CCC- change of bps +71 to +73 in gcvB (p𝑔𝑐𝑣𝐵^t1↑+71CCC)	This study
pGS649	pGS642 with a -TGT- to -AAA- change of bps +76 to +78 in gcvB (p𝑔𝑐𝑣𝐵^t1↑+76AAA)	This study
pGS653	pGS642 with a -TGTT- to -CCCA- change of bps +79 to +82 in gcvB (p𝑔𝑐𝑣𝐵^t1↑+79CCCA)	This study
pGS655	pGS642 with a -T- to -C- change of bp +79 in gcvB (𝑔𝑐𝑣𝐵^t1↑+79C)	This study
pGS656	pGS642 with a -G- to -A- change of bp +80 in gcvB (p𝑔𝑐𝑣𝐵^t1↑+80A)	This study
pGS680	pGS594 with a deletion from bp +74 to +82 in gcvB (p𝑔𝑐𝑣𝐵^Δ+74∶82)	This study
pGS682	pGS680 with a -TG- to -CA- change of bps +142 and +143 in gcvB (p𝑔𝑐𝑣𝐵^Δ+74∶82+142CA)	This study
pGS683	pGS680 with a -TG- to -CC- change of bps +159 and +160 in gcvB (p𝑔𝑐𝑣𝐵^Δ+74∶82+159CC)	This study
pGS684	pGS680 with a -TT- to -CC- change of bps +131 and +132 in gcvB (p𝑔𝑐𝑣𝐵^Δ+74∶82+131CC)	This study
pGS688	pGS680 with the 𝑔𝑐𝑣𝐵^t1↑ change (p𝑔𝑐𝑣𝐵^t1↑Δ+74∶82)	This study
pGS697	pGS680 with a -TG- to -CA- change of bps +142 and +143 and a -TG- to -CC- change of bps +159 and +160 in gcvB (p𝑔𝑐𝑣𝐵^Δ+74∶82+142CA+159CC)	This study
pGS698	pGS680 with a -TT- to -CC- change of bps +131 and +132 and a -TG- to -CA- change of bps +142 and +143 in gcvB (p𝑔𝑐𝑣𝐵^Δ+74∶82+131CC+142CA)	This study
pGS699	pGS680 with a -TT- to -CC- change of bps +131 and +132 and a -TG- to CC change of bps +159 and +160 in gcvB (p𝑔𝑐𝑣𝐵^Δ+74∶82+131CC+159CC)	This study
Phage
λgt2	λ cloning vector; cI857 repressor	[18]
λcycA-lacZ	λ vector carrying WT cycA-lacZ translational fusion	[2]
𝜆𝑐𝑦𝑐𝐴^−24GG-lacZ	λ vector carrying a 𝑐𝑦𝑐𝐴^−24GG-lacZ translational fusion with an -AC- to -GG- change at nts −24 and −25	This study
𝜆𝑐𝑦𝑐𝐴^−29G-lacZ	λ vector carrying a 𝑐𝑦𝑐𝐴^−29G-lacZ translational fusion with an -A- to -G- change at nt −29	This study
𝜆𝑐𝑦𝑐𝐴^−30T-lacZ	λ vector carrying a 𝑐𝑦𝑐𝐴^−39T-lacZ translational fusion with a -C- to -T- change at nt −30	This study

*All strains also carry the pheA905 thi araD129 rpsL150 relA1 deoC1 flbB5301 ptsF25 rbsR mutations.
**Numbering for gcvB mutations is based on the transcription initiation site as +1. Numbering for the cycA fusions and mutations is based on the A residue in the AUG translation initiation codon as +1 with bases upstream assigned negative values.