Table 1.
Representative CDSs differentially expressed in the rpoS mutant and the wild-type strain UK4 at the mRNA and protein levels.
| Locus taga | Protein accession | Function description | mRNA ΔrpoS/UK4 ratio (adjusted p-value)b | Protein ΔrpoS/UK4 ratio (p-value)c | Regulation type (mRNA/protein)d |
|---|---|---|---|---|---|
| TRANSCRIPTION FACTORS AND SIGNAL TRANSDUCTION | |||||
| HZ99_RS01135 | WP_038440714.1 | Acyl-homoserine-lactone synthase RhlI | 0.157 (2.51E-12) | – | Down/– |
| HZ99_RS01140 | WP_038440716.1 | Transcriptional regulator RhlR | 0.192 (2.38E-10) | – | Down/– |
| HZ99_RS01145 | WP_038440719.1 | Rhamnosyltransferase chain B, RhlB | 0.034 (1.36E-24) | – | Down/– |
| HZ99_RS01150 | WP_038440722.1 | Rhamnosyltransferase 1 subunit A, RhlA | 0.029 (3.31E-19) | – | Down/– |
| HZ99_RS01735 | WP_038440888.1 | LuxR family transcriptional regulator | 0.106 (1.78E-04) | – | Down/– |
| HZ99_RS01825 | WP_038440917.1 | RNA polymerase sigma factor | 0.176 (4.49E-05) | – | Down/– |
| HZ99_RS03980 | WP_038441499.1 | Fis family transcriptional regulator | 0.083 (4.47E-05) | – | Down/– |
| HZ99_RS09360 | WP_038442561.1 | DNA-binding transcriptional regulator BasR (PmrA) | 0.232 (7.59E-08) | – | Down/– |
| HZ99_RS09580 | WP_003178872.1 | Carbon storage regulator RsmA | 0.262 (6.78E-07) | – | Down/– |
| HZ99_RS09820 | WP_038442724.1 | RNA polymerase subunit sigma-24, RpoE | 0.265 (4.04E-02) | – | Down/– |
| HZ99_RS09895 | WP_038442747.1 | Methyl-accepting chemotaxis protein | 0.058 (1.43E-03) | 0.291 (4.20E-05) | Down/Down |
| HZ99_RS10650 | WP_038442895.1 | Diguanylate cyclase response regulator WspR | 0.329 (6.95E-03) | – | Down/– |
| HZ99_RS10655 | WP_038442896.1 | Chemotaxis-specific methylesterase WspF | 0.280 (1.11E-06) | 0.746 (3.24E-02) | Down / Down |
| HZ99_RS10660 | WP_038442897.1 | Chemotaxis sensor/effector fusion protein WspE | 0.301 (3.33E-04) | – | Down/– |
| HZ99_RS10665 | WP_038442898.1 | Chemotaxis protein WspD | 0.321 (7.73E-03) | – | Down/– |
| HZ99_RS10670 | WP_038442899.1 | Chemotaxis protein WspC | 0.306 (2.22E-02) | – | Down/– |
| HZ99_RS10675 | WP_038442901.1 | Chemotaxis protein WspB | 0.292 (2.76E-04) | – | Down/– |
| HZ99_RS10680 | WP_038442902.1 | Chemotaxis transducer WspA | 0.251 (1.05E-04) | 0.812 (6.07E-03) | Down/Down |
| HZ99_RS14415 | WP_017739508.1 | PrkA family serine protein kinase | 0.014 (3.29E-16) | 0.097 (2.78E-04) | Down/Down |
| HZ99_RS14470 | WP_038443829.1 | Bifunctional diguanylate cyclase/phosphodiesterase | 0.044 (2.50E-09) | – | Down/– |
| HZ99_RS15265 | WP_038444050.1 | ArsR family transcriptional regulator | – | 0.578 (2.84E-03) | –/Down |
| HZ99_RS16305 | WP_038444414.1 | DNA-binding response regulator | 0.512 (1.97E-02) | 0.795 (9.15E-03) | Down/Down |
| HZ99_RS19375 | WP_038445316.1 | Two-component system response regulator NtrC | 0.354 (2.64E-04) | 0.759 (1.09E-02) | Down/Down |
| HZ99_RS20755 | WP_038445694.1 | PAS domain-containing sensor histidine kinase | 0.037 (1.74E-09) | – | Down/– |
| HZ99_RS20770 | WP_038445699.1 | DNA-binding response regulator CitB | 0.129 (2.11E-07) | 0.574 (2.15E-03) | Down/Down |
| HZ99_RS23975 | WP_038446534.1 | Bifunctional diguanylate cyclase/phosphodiesterase | 0.073 (9.68E-06) | – | Down/– |
| HZ99_RS24460 | WP_038446651.1 | RNA polymerase sigma-H factor AlgU | – | 1.458 (1.78E-02) | -/Up |
| HZ99_RS25335 | WP_038446976.1 | Anti-anti-sigma factor HsbA | 0.087 (1.88E-04) | 0.182 (4.82E-05) | Down/Down |
| HZ99_RS25340 | WP_038446978.1 | HptB-dependent secretion and biofilm regulator HsbR | 0.090 (2.23E-03) | – | – |
| HZ99_RS25765 | WP_038447108.1 | Methyl-accepting chemotaxis protein | – | 0.565 (2.85E-03) | –/Down |
| POLYSACCHARIDE METABOLISM | |||||
| HZ99_RS00070 | WP_038440366.1 | Polysaccharide biosynthesis protein PslL | 0.215 (2.35E-08) | – | Down/– |
| HZ99_RS00075 | WP_038440367.1 | Acyltransferase | 0.169 (2.82E-11) | – | Down/– |
| HZ99_RS00080 | WP_038440369.1 | Polysaccharide biosynthesis protein PslJ | 0.161 (1.58E-11) | – | Down/– |
| HZ99_RS00085 | WP_038440370.1 | Polysaccharide biosynthesis protein PslI | 0.127 (4.49E-14) | 0.619 (1.95E-02) | Down/Down |
| HZ99_RS00090 | WP_038440371.1 | Polysaccharide biosynthesis protein PslH | 0.136 (1.51E-13) | – | Down/– |
| HZ99_RS00095 | WP_038440372.1 | Polysaccharide biosynthesis protein pslG | 0.098 (6.06E-18) | 0.577 (1.43E-02) | Down/Down |
| HZ99_RS00100 | WP_038440373.1 | Polysaccharide biosynthesis protein PslF | 0.117 (2.05E-13) | 0.684 (1.25E-02) | Down/Down |
| HZ99_RS00105 | WP_038440374.1 | Polysaccharide biosynthesis protein PslE | 0.102 (1.81E-16) | 0.590 (4.52E-03) | Down/Down |
| HZ99_RS00110 | WP_038440375.1 | Polysaccharide biosynthesis protein PslD | 0.085 (6.34E-17) | – | Down/– |
| HZ99_RS00115 | WP_038440377.1 | Polysaccharide biosynthesis protein PslC | 0.092 (2.69E-16) | 0.526 (1.20E-03) | Down/Down |
| HZ99_RS00120 | WP_038440378.1 | Polysaccharide biosynthesis protein PslB | 0.107 (9.57E-14) | 0.593 (2.05E-02) | Down/Down |
| HZ99_RS00125 | WP_038440379.1 | Polysaccharide biosynthesis protein PslA | 0.078 (3.34E-16) | – | Down/– |
| HZ99_RS03630 | WP_038441389.1 | Glycogen synthase GlgA | 0.355 (1.23E-04) | – | Down/– |
| HZ99_RS03635 | WP_038441390.1 | Malto-oligosyltrehalose trehalohydrolase TreZ | 0.266 (7.44E-06) | – | Down/– |
| HZ99_RS03640 | WP_038441391.1 | 4-alpha-glucanotransferase MalQ | 0.405 (2.76E-03) | – | Down/– |
| HZ99_RS03645 | WP_038441393.1 | Malto-oligosyltrehalose synthase TreY | 0.234 (1.78E-07) | – | Down/– |
| HZ99_RS03650 | WP_038441395.1 | Hypothetical protein | 0.365 (1.87E-03) | – | Down/– |
| HZ99_RS03655 | WP_038441396.1 | Glycogen debranching enzyme GlgX | 0.299 (2.46E-05) | 0.747 (4.89E-02) | Down/Down |
| HZ99_RS03670 | WP_038441402.1 | 1,4-alpha-glucan branching protein GlgB | 0.210 (1.57E-07) | – | Down/– |
| HZ99_RS03675 | WP_038441404.1 | Maltose alpha-D-glucosyltransferase TreS | 0.298 (1.60E-05) | – | Down/– |
| HZ99_RS03680 | WP_038441406.1 | Alpha-1,4-glucan—maltose-1-phosphate maltosyltransferase GlgE | 0.247 (6.95E-07) | – | |
| HZ99_RS10715 | WP_038442912.1 | Phosphoethanolamine transferase OpgE | 0.237 (2.95E-02) | 0.553 (1.08E-02) | Down/Down |
| HZ99_RS19405 | WP_038445324.1 | Maltodextrin phosphorylase GlgP | 0.190 (1.31E-09) | 0.553 (5.91E-03) | Down/Down |
| HZ99_RS23185 | WP_038446334.1 | Trehalose permease IIC protein | 0.554(5.91E-03) | –/Down | |
| INTRACELLULAR SECRETION AND EXTRACELLULAR STRUCTURES | |||||
| HZ99_RS00355 | WP_080727762.1 | Type V secretory pathway, adhesin AidA | 0.032 (3.29E-03) | - | Down/– |
| HZ99_RS03975 | WP_008603564.1 | FapF | 0.017 (3.21E-08) | 0.468 (2.66E-04) | Down/Down |
| HZ99_RS20775 | WP_038445702.1 | Hypothetical protein | 0.029 (6.35E-15) | – | Down/– |
| HZ99_RS20780 | WP_038445704.1 | Type II secretion system protein TadD | 0.018 (8.12E-10) | – | Down/– |
| HZ99_RS20785 | WP_038445705.1 | Pilus assembly protein TadC | 0.021 (2.26E-09) | – | Down/– |
| HZ99_RS20790 | WP_038445707.1 | Flp pilus assembly protein TadB | 0.022 (5.07E-09) | – | Down/– |
| HZ99_RS20795 | WP_038445708.1 | ATPase TadA | 0.020 (4.85E-11) | 0.100 (5.84E-04) | Down/Down |
| HZ99_RS20800 | WP_038445709.1 | Flp pilus assembly protein TadZ | 0.016 (3.03E-11) | 0.216 (2.83E-03) | Down/Down |
| HZ99_RS20805 | WP_038445710.1 | Type II/III secretion system protein RcpA | 0.017 (2.35E-08) | – | Down/– |
| HZ99_RS20810 | WP_038445713.1 | Flp pilus assembly protein RcpC | 0.010 (1.38E-14) | 0.217 (1.61E-03) | Down/Down |
| HZ99_RS20815 | WP_038445716.1 | Flp family type IVb pilin | 0.040 (9.64E-13) | – | Down/– |
| HZ99_RS20820 | WP_038445718.1 | Response regulator | 0.043 (7.89E-12) | – | Down/– |
| HZ99_RS20825 | WP_038445719.1 | Flp family type IVb pilin | 0.059 (6.93E-15) | – | Down/– |
| HZ99_RS20830 | WP_038445722.1 | Hemolysin activation/secretion protein FhaC | 0.017 (6.11E-10) | 0.380 (1.97E-03) | Down/Down |
| HZ99_RS21155 | WP_024015038.1 | Type II secretory pathway, component ExeA (predicted ATPase) | 0.088 (2.31E-11) | 0.201 (3.09E-04) | Down/Down |
| HZ99_RS24960 | WP_038446836.1 | HlyD family type I secretion periplasmic adaptor subunit | 0.073 (2.27E-09) | – | Down/– |
| HZ99_RS24965 | WP_038448190.1 | Type I secretion system permease/ATPase | 0.085 (7.92E-11) | – | Down/– |
| HZ99_RS24970 | WP_038446837.1 | Type I secretion outer membrane protein, TolC family | 0.019 (1.61E-04) | 0.310 (2.86E-04) | Down/Down |
| CELL WALL BIOGENESIS | |||||
| HZ99_RS02640 | WP_038441173.1 | LPS O-antigen chain length determinant protein | 0.297 (3.08E-06) | 0.800 (3.04E-02) | Down/Down |
| HZ99_RS09290 | WP_038442547.1 | UDP 4-amino-4-deoxy-L-arabinose aminotransferase | 0.064 (8.84E-04) | – | Down/– |
| HZ99_RS09295 | WP_038442548.1 | UDP 4-deoxy-4-formamido-L-arabinose transferase ArnC | 0.040 (2.47E-04) | – | Down/– |
| HZ99_RS09300 | WP_038442549.1 | Bifunctional UDP-glucuronic acid oxidase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase ArnA | 0.087 (2.13E-03) | 0.202 (1.00E-03) | Down/Down |
| HZ99_RS09305 | WP_038442550.1 | 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD | 0.069 (1.15E-06) | – | Down/– |
| HZ99_RS09310 | WP_038442551.1 | 4-amino-4-deoxy-L-arabinose transferase ArnT | 0.069 (5.68E-04) | – | Down/– |
| HZ99_RS09315 | WP_038442552.1 | 4-amino-4-deoxy-L-arabinose-phospho-UDP flippase ArnE | 0.175 (4.61E-02) | – | Down/– |
| HZ99_RS09325 | WP_038442554.1 | UDP-glucose 6-dehydrogenase | 0.100 (4.32E-06) | 0.442 (3.52E-03) | Down/Down |
| HZ99_RS26590 | WP_038447400.1 | Glycosyl transferase | – | 0.443 (1.87E-02) | –/Down |
| STRESS RESPONSES | |||||
| HZ99_RS02240 | WP_038441046.1 | Peroxiredoxin AhpC | – | 0.809 (2.96E-02) | –/Down |
| HZ99_RS13955 | WP_038443738.1 | Catalase KatE | 0.194 (5.59E-05) | 0.469 (2.68E-03) | Down/Down |
| HZ99_RS16790 | WP_028618516.1 | GlsB/YeaQ/YmgE family stress response membrane protein | 0.165 (2.28E-04) | – | Down/– |
| HZ99_RS17150 | WP_038444652.1 | RND divalent metal cation efflux transporter CzcA | 0.379 (2.52E-04) | – | Down/– |
| HZ99_RS17155 | WP_019334917.1 | RND divalent metal cation efflux membrane fusion protein CzcB precursor | 0.293 (3.53E-02) | – | Down/– |
| HZ99_RS17205 | WP_038444665.1 | Copper resistance protein A precursor PcoA | 0.185 (9.81E-03) | 0.621 (1.29E-03) | Down/Down |
| HZ99_RS17210 | WP_038444668.1 | Copper resistance protein B precursor PcoB | 0.195 (3.68E-02) | 0.757 (2.90E-02) | Down/Down |
| HZ99_RS17635 | WP_038444793.1 | Peroxiredoxin OsmC | 0.116 (1.73E-06) | 0.251 (4.43E-03) | Down/Down |
| HZ99_RS18120 | WP_038444941.1 | Multidrug export protein EmrA | 0.156 (4.07E-11) | – | Down/– |
| HZ99_RS18555 | WP_038445116.1 | RND triclosan efflux membrane fusion protein, TriA | 0.210 (1.11E-02) | – | Down/– |
| HZ99_RS18560 | WP_038445117.1 | RND triclosan efflux membrane fusion protein, TriB | 0.235 (1.13E-03) | 0.550 (1.04E-02) | Down/Down |
| HZ99_RS18565 | WP_038445119.1 | RND triclosan efflux membrane fusion protein, TriC | 0.184 (4.00E-04) | – | Down/– |
| HZ99_RS22450 | WP_038446132.1 | Glutathione peroxidase | – | 0.763 (0.00123) | –/Down |
| HZ99_RS26805 | WP_029298005.1 | Universal stress protein UspA | 0.248 (1.72E-07) | – | Down/– |
| AMINO ACID AND BIOGENIC AMINE METABOLISM | |||||
| HZ99_RS02405 | WP_038441100.1 | Spermidine synthase | 0.115 (1.56E-05) | – | Down/– |
| HZ99_RS04195 | WP_038441535.1 | Lysine decarboxylase | 0.191 (1.23E-05) | – | Down/– |
| HZ99_RS06735 | WP_038441955.1 | Methionine gamma-lyase | – | 0.482 (8.69E-03) | –/Down |
| HZ99_RS07550 | WP_038442095.1 | Agmatine deiminase | 0.125 (6.06E-07) | – | Down/– |
| HZ99_RS10175 | WP_038442810.1 | Arginine deiminase | – | 0.797 (7.34E-03) | –/Down |
| HZ99_RS10185 | WP_038442812.1 | Carbamate kinase ArcC | 0.468 (4.14E-02) | 0.803 (2.35E-03) | Down/Down |
| HZ99_RS14340 | WP_038443794.1 | Spermidine/putrescine ABC transporter substrate-binding protein | – | 0.524 (2.47E-02) | –/Down |
| HZ99_RS14900 | WP_038443918.1 | Glycine cleavage system protein R | 0.194 (9.81E-05) | 0.391 (9.62E-03) | Down/Down |
| HZ99_RS15270 | WP_038444052.1 | Methionine adenosyltransferase | 0.482 (1.05E-02) | 0.580 (1.57E-03) | Down/Down |
| HZ99_RS20705 | WP_038445679.1 | Arginine decarboxylase SpeA | 0.397 (4.55E-04) | 0.821 (1.61E-02) | Down/Down |
| HZ99_RS22590 | WP_038446180.1 | Glu/Leu/Phe/Val dehydrogenase | 0.083 (2.60E-10) | 0.293 (3.62E-04) | Down/Down |
| HZ99_RS26135 | WP_038447234.1 | Spermidine/putrescine ABC transporter ATP-binding protein | 0.163 (3.69E-04) | – | Down/– |
| HZ99_RS26140 | WP_029292823.1 | ABC-type spermidine/putrescine transport system, permease component II | 0.169 (1.39E-02) | – | Down/– |
| HZ99_RS26155 | WP_038447240.1 | Spermidine/putrescine-binding periplasmic protein | 0.110 (1.70E-02) | 0.461 (8.83E-03) | Down/Down |
| OXIDATIVE PHOSPHORYLATION | |||||
| HZ99_RS17715 | WP_038444813.1 | Cytochrome b559 subunit alpha | 0.029 (1.72E-07) | 0.194 (9.29E-05) | Down/Down |
| HZ99_RS17720 | WP_038444815.1 | Cytochrome c oxidase subunit I | 0.035 (1.81E-03) | – | Down/– |
| HZ99_RS17725 | WP_038444816.1 | Cytochrome c oxidase assembly protein | 0.032 (9.73E-04) | – | Down/– |
| HZ99_RS17730 | WP_038444818.1 | Cytochrome c oxidase subunit III | 0.044 (2.36E-04) | – | Down/– |
| HZ99_RS17740 | WP_038444821.1 | Cytochrome oxidase biogenesis protein Surf1,facilitates heme A insertion | 0.026 (2.98E-07) | – | Down/– |
| HZ99_RS17745 | WP_038448109.1 | Hypothetical protein | 0.042 (7.68E-06) | – | Down/– |
| HZ99_RS17750 | WP_038444822.1 | Cytochrome b561 | 0.051 (4.43E-05) | – | Down/– |
| HZ99_RS17755 | WP_038444823.1 | Protoheme IX farnesyltransferase | 0.044 (4.04E-04) | – | Down/– |
| HZ99_RS23395 | WP_038446389.1 | NADH:flavin oxidoreductase/NADH oxidase | 0.017 (4.36E-07) | 0.275 (5.50E-06) | Down/Down |
| SULFUR METABOLISM | |||||
| HZ99_RS15945 | WP_003213899.1 | Transporter | 6.011 (3.59E-04) | Up/– | |
| HZ99_RS15950 | WP_038444290.1 | Aliphatic sulfonates ABC transporter ATP-binding protein SsuB | 5.495 (5.07E-04) | Up/– | |
| HZ99_RS15955 | WP_038444293.1 | Alkanesulfonate transporter permease subunit SsuC | 4.988 (3.08E-02) | Up/– | |
| HZ99_RS18395 | WP_038445051.1 | Sulfate-binding protein precursor | - | 1.394 (4.14E-02) | –/Up |
| HZ99_RS18400 | WP_032856532.1 | Sulfate ABC transporter permease subunit CysT | 2.407 (1.39E-02) | Up/– | |
| HZ99_RS18410 | WP_038445056.1 | Sulfate ABC transporter ATP-binding protein CysA | 2.391 (6.81E-03) | Up/– | |
| HZ99_RS18930 | WP_038445174.1 | Taurine dioxygenase TauD | 2.522 (2.42E-02) | Up/– | |
| HZ99_RS18940 | WP_038445178.1 | Taurine transporter ATP-binding subunit TauB | – | 1.597 (2.31E-04) | –/Up |
| HZ99_RS18945 | WP_038445179.1 | Taurine ABC transporter substrate-binding protein TauA | – | 1.319 (2.97E-02) | –/Up |
| HZ99_RS27240 | WP_038447698.1 | Methanesulfonate sulfonatase MsuD | – | 1.447 (6.49E-03) | –/Up |
a
CDSs belonging to a putative operon are marked with a box.
b, c, d
The symbol “–” indicates that the expression of the gene was not detected or was not significantly different between the rpoS mutant and wild-type.