. 2014 Sep 2;5(5):e01683-14. doi: 10.1128/mBio.01683-14

TABLE 2 .

Fold changes in the transcript abundance of selected genes due to the deletion of gacS, salA, or rpoN

Locus	Gene	Function	Fold change in transcript abundance^a
			Basal			Epiphytic sites			Apoplastic sites
			gacS	salA	rpoN	gacS	salA	rpoN	gacS	salA	rpoN
rsmY^b,c	rsmY	Regulation	−6.3	−4.3	1.3	−6.0	−4.7	1.4	−19.5	−12.1	1.1
rsmZ^c	rsmZ	Regulation	−1.5	−1.2	−1.1	−1.5	1.2	1.2	−2.0	2.0	−7.5
sRNA_P16	rgsA	Regulation	1.0	1.0	−1.6	−3.1	−2.5	3.2	−1.6	−1.1	−1.2
Psyr_2601	salA	Regulation	−2.2	D	9.1	−9.0	D	−1.8	−7.6	D	1.6
Psyr_2607	syrF	Regulation	−2.4	−2.3	44.5	−8.5	−6.7	−4.7	−15.2	−6.8	2.7
Psyr_2611	syrB1	Syringomycin synthesis	−1.5	−1.6	54.7	−12.5	−10.5	−5.1	−34.5	−21.7	2.8
Psyr_2615	sypB	Syringopeptin synthesis	1.1	1.0	4.7	−1.9	−2.7	−1.7	−6.8	−3.5	4.0
Psyr_3041	lasB	Protease (elastin)	−3.0	−3.0	1.2	−4.7	−5.7	−2.7	−5.5	−10.0	−1.8
Psyr_3163	aprA	Alkaline protease	−29.5	−22.9	2.6	−28.9	−26.8	−1.7	−36.1	−41.5	2.8
Psyr_3129	rhlA	HAA synthesis	−3.0	−2.5	15.8	−4.3	−3.6	1.6	−6.9	−3.3	1.9
Psyr_2576	syfA	Syringafactin synthesis	1.0	−1.1	3.9	−2.0	−2.6	−1.2	−2.5	−2.3	6.6
Psyr_2577	syfB	Syringafactin synthesis	1.1	−1.2	1.8	−2.5	−2.9	−1.2	−5.0	−3.4	6.6
Psyr_2575	syfR	Regulation	−3.2	−3.3	6.4	−3.0	−3.6	−1.2	−4.1	−2.9	1.6
Psyr_1621	ahlI	3-oxo-C₆-HSL synthase	−6.2	−6.5	1.2	−2.9	−2.5	−1.1	−5.6	−4.3	−3.1
Psyr_1622	ahlR	Quorum regulator	−4.1	−4.2	−1.2	−4.3	−2.7	1.5	−4.1	−2.7	−1.6
Psyr_1059	algE	Alginate synthesis	−3.7	−1.8	−3.0	1.3	1.0	−3.6	−1.8	−2.7	4.5
Psyr_3301	pslA	Psl synthesis	−1.6	−2.3	1.1	−3.3	−3.1	−1.7	−3.6	−2.4	3.7
Psyr_0754	lsc1	Levansucrase	−2.7	−3.4	−1.8	1.8	−1.2	−1.6	−1.4	−5.1	1.3
Psyr_1704	sylC	Syringolin A synthesis	−1.7	−1.6	6.4	−2.1	−2.0	−1.2	−9.8	−6.7	2.8
Psyr_5009		Secondary metabolite synthesis	−5.3	−4.2	2.1	−3.9	−3.4	−1.2	−4.4	−2.1	1.4
Psyr_4314		Secondary metabolite synthesis	−1.4	−1.3	4.0	−4.8	−3.7	−3.9	−17.7	−8.7	2.5
Psyr_1374	rpoS	Sigma factor	−8.7	−7.0	2.3	−7.3	−6.1	1.6	−8.8	−10.8	2.5
Psyr_0749	fadD	Fatty acid metabolism	−7.1	−7.6	−1.2	−45.1	−33.8	−2.4	−57.1	−40.3	1.1
Psyr_3185	cspD	Cold shock protein	−3.6	−1.7	2.6	−4.5	−2.7	2.6	−3.5	−1.9	1.1
Psyr_1217	hrpL	T3SS regulation	−1.6	−1.8	1.0	2.4	2.0	−1.2	2.9	4.2	−3.7
Psyr_1192	hrpA2	T3SS pilus	−1.6	−1.9	−1.1	4.2	2.9	−2.6	12.7	4.5	−2.0
Psyr_4919	avrPto1	T3SS effector protein	−1.1	−2.1	−3.0	10.4	5.2	−8.7	28.1	8.6	−9.6
Psyr_2629	ppkA	T6SS-associated kinase	−6.3	−8.2	1.0	−5.0	−3.6	−2.2	−2.3	−1.4	−1.2

^{^a}

Values shown are the fold change in transcript abundance in the mutants lacking gacS, salA, or rpoN relative to transcript abundance in the wild type. The values in boldface type exhibited a significant change in transcript abundance (q value of <0.01); few genes showed significant changes in the cells from apoplastic sites due to the high variation among replicate samples in the lab II data set (see Fig. S1 in the supplemental material). For results in all of the environmental conditions evaluated, see Table S2. D, the gene was deleted in this mutant.

^{^b}

rsmY also showed reduced transcript abundance in the ∆gacS and ∆salA mutants in most of the stress conditions in vitro (Table S2).

^{^c}

Comparisons to sRNAs in other pseudomonads indicated that each of these sRNAs was smaller than those predicted using SIPHT (38), with rsmY, rsmZ, and rgsA encoded as orthologs of PSPTO_5647, PSPTO_5652, and PSPTO_5600, respectively.