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. 2020 May 19;5(3):e00204-20. doi: 10.1128/mSystems.00204-20

TABLE 1.

Selected genes of interest with differential expression in the PA0805.1 overexpression strain compared to EV by RNA-Seq and/or proteomicsa

Category Locus tag Name Product name RNA-Seq
 Proteomics
FC Padj FC P
Transcriptional regulators, two-component systems, sigma and anti-sigma factors PA0150 Anti-sigma factor −1.71 2.9E−02
PA0178 Probable two-component sensor 1.83 8.5E−06
PA0179 Probable two-component response regulator 2.02 2.0E−06
PA0268 Probable transcriptional regulator 1.52 3.0E−03
PA0408 pilG Twitching motility protein −2.09 2.8E−17 −1.52 2.5E−03
PA0409 pilH Twitching motility protein −2.42 2.2E−29 −1.64 1.2E−02
PA0416 chpD Probable transcriptional regulator −1.96 9.0E−07
PA0459 clpD Probable Clpa/B protease ATP binding subunit 1.70 3.3E−04 1.89 9.0E−04
PA0471 fiuR Sigma factor −1.80 4.6E−04
PA0472 fiuI Sigma factor related −2.03 4.2E−04
PA0479 Probable transcriptional regulator 1.57 2.5E−04
PA0535 Probable transcriptional regulator −1.69 1.2E−03
PA0612 ptrB Repressor 2.52 6.3E−04
PA0757 Probable two-component sensor −1.53 9.9E−04
PA0763 mucA Anti-sigma factor 1.68 5.7E−05
PA0807 ampDh3 Regulator of β-lactamase activity 2.18 8.3E−07
PA0929 Two-component response regulator −1.68 1.9E−03
PA0930 Two-component sensor −1.61 1.5E−02
PA0942 Probable transcriptional regulator 1.54 1.2E−03
PA0964 pmpR pqsR-mediated PQS regulator −1.64 8.6E−08 −1.18 3.2E−04
PA1099 fleR Two-component response regulator 1.52 3.9E−08
PA1136 Probable transcriptional regulator 1.75 1.4E−04
PA1159 Probable cold shock protein (DNA-binding domain) −1.44 2.4E−02
PA1363 ECF sigma factor −1.69 2.4E−03
PA1364 Probable transmembrane sensor −1.88 1.3E−02
PA1397 Probable two-component response regulator −1.68 5.3E−05
PA1405 Probable helicase −1.69 4.9E−04
PA1423 bdlA Chemotaxis transducer 1.94 1.4E−06
PA1430 lasR Transcriptional regulator −1.28 4.9E−02
PA1431 rsaL Regulatory protein 1.70 6.8E−04 1.25 8.3E−03
PA1619 Probable transcriptional regulator −1.50 1.8E−03
PA1705 pcrG Regulator in type III secretion −9.28 5.4E−12
PA1707 pcrH Regulatory protein −8.60 4.9E−26
PA1713 exsA Transcriptional regulator −4.77 6.3E−62
PA1714 exsD Negative regulator −3.75 8.1E−34 −1.87 8.1E−04
PA1785 nasT Regulatory protein 1.76 3.3E−02 −1.26 1.3E−04
PA1859 Probable transcriptional regulator 1.55 5.8E−04
PA1945 Probable transcriptional regulator 1.53 3.6E−03
PA2126 cgrC CupA gene regulator C 2.18 1.2E−05
PA2126.1 cgrB CupA gene regulator B 1.78 7.6E−03
PA2127 cgrA CupA gene regulator A 1.80 4.3E−06
PA2177 Probable sensor/response regulator hybrid 1.77 2.5E−04
PA2227 vqsM AraC-type transcriptional regulator 1.77 3.3E−06
PA2258 ptxR Transcriptional regulator 2.15 1.2E−05
PA2259 ptxS Transcriptional regulator 1.82 1.6E−04
PA2273 soxR Regulatory protein 2.38 1.5E−09
PA2276 Probable transcriptional regulator 3.41 2.8E−38 1.27 9.3E−04
PA2277 arsR Regulatory protein 2.28 1.9E−06
PA2376 Probable transcriptional regulator 1.56 1.4E−03
PA2388 fpvR Regulatory protein −1.30 1.2E−02
PA2467 foxR Anti-sigma factor −1.62 1.3E−02
PA2523 czcR Regulatory protein 2.32 4.9E−08
PA2524 czcS Regulatory protein 2.24 1.2E−04
PA2571 Probable two-component sensor 2.02 3.1E−06
PA2572 Probable two-component response regulator 1.86 8.1E−06 1.29 1.4E−02
PA2577 Probable transcriptional regulator 1.70 3.4E−05
PA2620 clpA ATP-binding protease component 1.60 4.8E−06 1.16 1.1E−02
PA2622 cspD Cold shock protein 1.80 1.5E−05 1.25 6.0E−03
PA2696 Probable transcriptional regulator 1.53 4.5E−03
PA2771 Diguanylate cyclase 1.84 3.8E−09
PA2846 Probable transcriptional regulator 1.64 7.3E−03
PA2849 ohrR Regulatory protein 1.63 2.2E−05 1.11 2.8E−02
PA2889 atvR Atypical virulence-related response regulator 1.55 7.7E−04
PA3006 psrA Transcriptional regulator 1.09 3.4E−02
PA3007 lexA Repressor protein 1.84 5.6E−23 1.10 6.1E−03
PA3078 cprS Sensor kinase −1.50 1.3E−03
PA3160 wzz O-antigen chain length regulator 1.27 2.3E−02
PA3174 hutR Regulatory protein −1.66 1.8E−02
PA3266 capB Cold acclimation protein B −1.54 1.1E−04 −1.67 3.2E−02
PA3346 hsbR HptB-dependent secretion and biofilm regulator 1.78 3.6E−09 1.22 1.2E−02
PA3347 hsbA HptB-dependent secretion and biofilm anti-anti-sigma factor 1.66 4.9E−05
PA3477 rhlR Transcriptional regulator 1.77 1.9E−05 1.17 1.9E−02
PA3622 rpoS Sigma factor 1.75 1.4E−09 1.17 5.1E−03
PA3899 fecI Regulatory protein −1.73 1.3E−02
PA3946 rocS1 Two-component sensor 1.74 4.3E−07
PA3947 rocR Regulatory protein 1.57 7.5E−06
PA4070 Probable transcriptional regulator 1.52 3.3E−02
PA4074 Probable transcriptional regulator 2.20 2.7E−03
PA4080 Probable response regulator 1.54 5.3E−04
PA4203 nmoR Regulatory protein 1.50 4.6E−02
PA4218 ampP Regulator of β-lactamase activity −1.77 1.5E−05 −1.18 1.8E−02
PA4219 ampO Regulator of β-lactamase activity −1.76 4.3E−04
PA4288 Probable transcriptional regulator 2.20 1.9E−07
PA4293 pprA Two-component sensor 2.22 5.0E−16 1.31 3.8E−03
PA4296 pprB Two-component response regulator 1.82 6.4E−07 1.12 1.1E−03
PA4315 mvaT Transcriptional regulator mvat, P16 subunit 1.26 2.6E−02
PA4396 Two-component response regulator −2.15 4.8E−11
PA4464 ptsN Nitrogen-regulatory IIA protein 1.74 1.6E−10
PA4493 roxR Regulatory protein 1.26 2.5E−02
PA4546 pilS Two-component sensor 1.28 3.1E−03
PA4600 nfxB Transcriptional regulator 1.25 4.7E−02
PA4601 morA Motility regulator −1.54 1.2E−12
PA4624 cdrB Cyclic diguanylate-regulated TPS partner B 2.27 1.4E−31 1.25 1.7E−02
PA4625 cdrA Cyclic diguanylate-regulated TPS partner A 4.18 7.6E−58
PA4769 Probable transcriptional regulator 1.35 2.8E−02
PA4781 Cyclic di-GMP phosphodiesterase 1.58 2.0E−04
PA4843 gcbA Regulatory protein −1.97 4.4E−18
PA4886 Probable two-component sensor −1.65 2.3E−02
PA4916 nrtR Nudix-related transcriptional regulator 1.60 1.8E−08 1.18 4.6E−03
PA4959 fimX Response regulator and diguanylate cyclase −1.54 2.7E−07
PA4969 cpdA Cyclic AMP phosphodiesterase −1.80 1.6E−08
PA5117 typA Regulatory protein −1.56 2.3E−05
PA5261 algR Alginate biosynthesis regulatory protein 1.57 1.4E−05
PA5274 rnk Nucleoside diphosphate kinase regulator −1.53 1.5E−05 −1.26 3.5E−02
PA5356 glcC Transcriptional regulator 1.74 7.2E−07
PA5380 gbdR Regulatory protein 1.58 2.5E−02
Multidrug efflux systems PA2018 mexY Resistance-nodulation-cell division (RND) multidrug efflux transporter 1.79 6.5E−04
PA2019 mexX RND multidrug efflux membrane fusion protein 1.91 4.9E−07 1.53 5.4E−04
PA4205 mexG Hypothetical protein 1.76 2.0E−14 1.59 9.1E−05
PA4206 mexH Probable RND efflux membrane fusion protein 1.71 7.2E−13 1.11 2.8E−02
Motility and related genes PA0020 tsaP T4P secretin-associated protein −1.97 6.8E−11 −1.35 1.0E−03
PA0410 pilI Twitching motility protein −2.37 1.1E−16 −1.48 6.8E−04
PA0411 pilJ Twitching motility protein −2.76 4.3E−24 −1.49 4.8E−05
PA0412 pilK Methyltransferase −2.40 2.3E−19
PA0413 chpA Pilus-related chemotactic signal transduction system component −2.44 1.9E−33 −1.24 3.8E−06
PA0414 chpB Probable methylesterase −2.31 3.1E−24
PA0415 chpC Probable chemotaxis protein −2.18 2.0E−13
PA0417 chpE Probable chemotaxis protein −2.77 7.8E−04
PA0499 Probable pilus assembly chaperone 1.87 3.1E−03
PA1077 flgB Flagellar basal-body rod protein 1.66 5.3E−11
PA1078 flgC Flagellar basal-body rod protein 1.70 5.1E−10
PA1079 flgD Flagellar basal-body rod modification protein 1.56 8.1E−09
PA1080 flgE Flagellar hook protein 1.58 9.5E−11
PA1081 flgF Flagellar basal-body rod protein 1.65 5.1E−11
PA1082 flgG Flagellar basal-body rod protein 1.57 4.5E−07
PA1084 flgI Flagellar P-ring protein precursor 1.53 1.6E−08
PA1085 flgJ Flagellar protein 1.54 2.4E−06
PA1092 fliC Flagellin type B 1.55 4.7E−06
PA1094 fliD Flagellar capping protein 1.53 4.9E−06
PA1100 fliE Flagellar hook-basal body complex protein 1.76 6.3E−08
PA1101 fliF Flagellar M-ring outer membrane protein precursor 1.52 3.5E−11
PA1130 rhlC Rhamnosyltransferase 2 1.56 5.8E−04
PA1452 flhA Flagellar biosynthesis protein 1.28 1.3E−02
PA3350 Hypothetical protein 1.62 3.1E−15 1.17 4.2E−03
PA3351 flgM Flagellar anti-sigma factor 1.52 1.2E−07
PA3478 rhlB Rhamnosyltransferase chain B 2.39 3.0E−04
PA3479 rhlA Rhamnosyltransferase chain A 2.55 1.1E−04
PA3526 motY Flagellar motor protein 1.60 2.3E−07
PA4085 cupB2 Chaperone 1.52 3.7E−02
PA4294 Hypothetical protein 2.32 1.4E−20
PA4295 fppA Flp prepilin peptidase A 1.68 9.8E−05
PA4297 tadG Putative Tad-like Flp pilus-assembly protein 1.53 1.1E−02
PA4298 Hypothetical protein 2.25 1.9E−07
PA4299 tadD Flp pilus assembly lipoprotein 1.89 1.4E−06 1.23 3.0E−03
PA4300 tadC Flp pilus assembly protein TadC 1.78 1.2E−05 1.29 8.1E−03
PA4301 tadB Flp pilus assembly protein 1.95 1.5E−06
PA4302 tadA ATPase 1.93 2.8E−08 1.20 5.0E−02
PA4303 tadZ Pilus assembly protein 2.09 5.3E−11 1.22 1.4E−02
PA4304 rcpA Secretin 1.97 1.3E−10
PA4305 rcpC Flp pilus assembly protein 2.12 8.4E−10
PA4306 flp Type IVb pilin 1.84 1.4E−03
PA4525 pilA Type 4 fimbrial precursor −1.64 2.0E−04 −1.30 3.4E−03
PA4528 pilD Type 4 prepilin peptidase −1.84 1.1E−08
PA4550 fimU Type 4 fimbrial biogenesis protein −1.74 2.0E−06 −1.11 4.9E−02
PA4551 pilV Type 4 fimbrial biogenesis protein −1.99 9.3E−07 −1.10 1.7E−02
PA4552 pilW Type 4 fimbrial biogenesis protein −1.72 9.2E−08 −1.22 2.4E−03
PA4553 pilX Type 4 fimbrial biogenesis protein −1.63 1.4E−04
PA4554 pilY1 Type 4 fimbrial biogenesis protein −1.59 9.6E−08
PA4555 pilY2 Type 4 fimbrial biogenesis protein −1.51 6.9E−05 −1.34 7.3E−03
PA4556 pilE Type 4 fimbrial biogenesis protein −1.64 9.4E−03
PA4648 cupE1 Pilin subunit 2.56 2.7E−16
PA4649 cupE2 Pilin subunit 2.06 1.8E−12
PA4650 cupE3 Pilin subunit 1.91 1.9E−06
PA4651 cupE4 Pilin assembly chaperone 2.00 5.2E−20 1.28 1.3E−03
PA4652 cupE5 Fimbrial usher protein 1.66 1.7E−07
PA4653 cupE6 Adhesin-like protein 1.69 1.1E−06
PA4959 fimX Diguanylate cyclase/phosphodiesterase −1.54 2.7E−07
PA5040 pilQ Type 4 fimbrial biogenesis outer membrane protein −1.63 8.0E−11 −1.38 4.7E−03
PA5041 pilP Type 4 fimbrial biogenesis protein −1.70 1.2E−08
PA5042 pilO Type 4 fimbrial biogenesis protein −1.67 2.6E−12 −1.26 9.0E−04
PA5043 pilN Type 4 fimbrial biogenesis protein −1.70 2.1E−10 1.77 6.6E−04
PA5044 pilM Type 4 fimbrial biogenesis protein −1.53 1.5E−10 −1.27 5.6E−03
Type VI secretion system PA0071 tagR1 FGE-sulfatase domain-containing protein 1.37 1.8E−03
PA0075 pppA Serine/threonine protein phosphatase 1.45 1.1E−02
PA0076 tagF1 Type VI secretion-associated protein 1.56 1.5E−02
PA0077 icmF1 Type VI secretion protein 1.37 4.7E−04
PA0078 tssL1 Type VI secretion system protein 1.59 1.3E−03 1.31 5.6E−03
PA0079 tssK1 Type VI secretion protein 1.58 1.4E−04 1.40 3.1E−03
PA0080 tssJ1 Type VI secretion protein 1.51 1.7E−07
PA0082 tssA1 Type VI secretion protein 1.52 4.1E−05 1.48 2.7E−03
PA0083 tssB1 Type VI secretion protein 1.72 2.8E−06
PA0084 tssC1 Type VI secretion protein 1.58 5.7E−04 1.52 4.7E−03
PA0085 hcp1 Type VI secretion system effector 1.74 3.9E−05 2.14 4.5E−04
PA0086 tagJ1 Type VI secretion system 1.74 1.6E−04
PA0087 tssE1 Type VI secretion system lysozyme-like protein 1.92 1.7E−04
PA0088 tssF1 Type VI secretion protein 1.58 3.7E−03
PA0090 clpV1 Chaperone 1.59 1.5E−03 1.54 3.4E−03
PA0091 vgrG1 Type VI secretion system tip protein 1.52 6.0E−03 1.23 2.4E−04
PA0094 eagT6 Chaperone 1.38 4.7E−04
PA0095 Type VI secretion protein 1.57 4.4E−09
PA0096 Hypothetical protein 2.11 1.4E−06
PA0097 Hypothetical protein 1.63 2.0E−07
PA0098 Hypothetical protein 1.67 6.2E−04
PA0099 Type vi effector protein 1.57 6.4E−06
PA0100 Hypothetical protein 1.52 2.0E−06 1.29 4.4E−04
PA1659 hsiF2 Type VI secretion system lysozyme-like protein 1.61 1.3E−04
PA1661 hsiH2 Type VI secretion protein 1.53 8.1E−03
PA1666 lip2 Type VI secretion system lipoprotein 1.33 1.8E−04
PA2361 icmF3 Type VI secretion protein 1.52 1.6E−05
PA2362 dotU3 Type VI secretion protein 1.89 1.1E−05
PA2363 hsiJ3 Type VI secretion protein 1.71 1.8E−09
PA2364 lip3 Type VI secretion protein 1.55 7.4E−05
PA2365 hsiB3 Type VI secretion protein 1.86 7.4E−09
PA2366 hsiC3 Type VI secretion protein 1.88 1.8E−07
PA2367 hcp3 Type VI secretion system effector 1.76 2.2E−06
PA2368 hsiF3 Type VI secretion protein 1.68 3.1E−03
PA2369 hsiG3 Type VI secretion protein 1.92 3.2E−11
PA2370 hsiH3 Type VI secretion protein 2.20 1.9E−06
PA2371 clpV3 Type VI secretion system ATPase 1.65 9.5E−07
PA2372 Hypothetical protein 1.69 1.4E−05
PA2373 vgrG3 Type VI secretion protein 1.68 4.7E−07
PA3486 vgrG4b Type VI secretion protein 1.69 6.9E−04
PA5266 vgrG6 Type VI secretion protein 1.89 7.3E−04
Other virulence factors PA0051 phzH Potential phenazine-modifying enzyme 2.53 9.4E−13
PA0122 rahU Hemolysin 2.30 3.0E−07 2.04 1.4E−02
PA1871 lasA LasA protease precursor 1.68 2.0E−04
PA1899 phzA2 Probable phenazine biosynthesis protein 1.70 2.6E−08
PA1900 phzB2 Probable phenazine biosynthesis protein 1.95 3.0E−10 1.25 4.3E−02
PA1901 phzC2 Phenazine biosynthesis protein 1.85 2.2E−06 1.44 4.5E−03
PA1903 phzE2 Phenazine biosynthesis protein 1.24 7.2E−04
PA1905 phzG2 Probable pyridoxamine 5′-phosphate oxidase 1.53 2.7E−05 1.16 9.7E−03
PA2231 pslA Undecaprenyl-phosphate glucose phosphotransferase 1.85 1.3E−09 1.29 2.2E−03
PA2232 pslB Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase 1.80 8.7E−12 1.34 6.5E−03
PA2233 pslC Putative glycosyl transferase 1.58 5.4E−09 1.14 4.5E−02
PA2234 pslD Polysaccharide export protein 1.71 4.9E−18 1.29 5.6E−03
PA2235 pslE Psl exopolysaccharide biosynthesis 1.68 2.6E−09 1.19 4.8E−03
PA2236 pslF Glycosyl transferase 1.62 1.4E−07
PA2237 pslG Beta-xylosidase 1.52 1.4E−14 1.19 4.1E−03
PA2238 pslH Glycosyl transferase 1.71 1.1E−06 1.28 1.8E−03
PA2239 pslI Psl exopolysaccharide biosynthesis 1.55 7.4E−05 1.13 4.6E−02
PA2243 pslM Hypothetical protein 1.73 5.1E−03
PA2244 pslN Hypothetical protein 1.88 8.2E−03
PA2570 lecA Galactose-binding lectin 7.32 2.4E−08 2.41 3.4E−03
PA3361 lecB Fucose-binding lectin PA-IIL 2.86 1,2E−07
PA3540 algD GDP-mannose 6-dehydrogenase 7.13 2.9E−09
PA3541 alg8 Alginate biosynthesis protein 2.79 4.7E−05
PA3542 alg44 Alginate biosynthesis protein 2.11 2.7E−02
PA3544 algE Alginate production outer membrane protein 2.73 1.8E−04
PA3545 algG Alginate-c5-mannuronan-epimerase 2.41 9.7E−05
PA3547 algL Poly(beta-d-mannuronate) lyase precursor 2.03 3.5E−02
PA3548 algI Alginate o-acetyltransferase 1.80 3.9E−02
PA3550 algF Alginate o-acetyltransferase 1.74 4.7E−02
PA3551 algA Phosphomannose isomerase/GDP-d-mannose pyrophosphorylase 1.82 1.3E−03
PA3724 lasB Elastase 1.64 1.7E−07
PA4175 piv Protease IV 1.86 1.7E−05
PA4212 phzC1 Phenazine biosynthesis protein 1.44 4.5E−03
PA4213 phzD1 Phenazine biosynthesis protein 1.20 1.4E−03
PA4214 phzE1 Phenazine biosynthesis protein 1.24 7.2E−04
a

Categories of interest include regulators, multidrug efflux, motility, type VI secretion system,and other virulence factors. Cutoffs used were P value of ≤0.05, absolute FC of ≥1.5 for RNA-Seq, and absolute FC of ≥1.25 for proteomics, although proteins with FC of ≤1.25 are also shown if there was a corresponding RNA-Seq or qRT-PCR value. n ≥ 3. Padj, adjusted P value.