Skip to main content

Advertisement

Table 2 Virulence plasmid genes differentially expressed in response to anaerobic conditions

From: RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri

ORF IDab Gene Description RNA-seqclog2FC RNA-seqclog2FC FRT-seqclog2FC
    WT no O2/O2 Δfnr/WT no O2 Δfnr/WT no O2
pWR501_0265 yigB hypothetical protein 2.56   
pWR501_0225 ospI T3SS effector 2.00 -2.21  
pWR501_0250 shf peptidoglycan deacetylase 1.24 -3.42 -1.30
pWR501_0251 rfbU glycosiltransferase 1.21 -1.65 -1.16
pWR501_0252 virK virulence protein 1.15 -2.16 -1.03
pWR501_0039 parA plasmid segregation protein 1.13   
pWR501_0253 msbB acyltransferase 1.07 -3.03 -1.08
pWR501_0074 sepA secreted protease -1.12 1.34 1.52
pWR501_0177   hypothetical protein -1.55   1.04
pWR501_0283 ipaH1.4 T3SS effector -1.56   
pWR501_0175   hypothetical protein -1.58   2.29
pWR501_0176   hypothetical protein -1.76   2.02
pWR501_0015   hypothetical protein -2.00 1.52 1.05
pWR501_0002   putative resolvase -2.04 1.97  
pWR501_0007   hypothetical protein -2.25 1.63  
pWR501_0014   hypothetical protein -2.25 1.60 1.27
pWR501_0192 virG invasion protein -2.25   2.36
pWR501_0144 ipgF unknown function -2.38   3.20
pWR501_0051 virF transcriptional activator of virulence -2.47   
pWR501_0006   hypothetical protein -2.54   
pWR501_0143 ipgE chaperon -2.55   3.39
pWR501_0146 mxiH T3SS component -2.56 1.55 4.10
pWR501_0122   hypothetical protein -2.58 1.53 1.95
pWR501_0121   hypothetical protein -2.65   
pWR501_0191 virA T3SS effector -2.66   2.42
pWR501_0147 mxiI T3SS component -2.80 2.00 4.01
pWR501_0013 mkaD mouse killing factor -2.81 1.97 3.33
pWR501_0145 mxiG T3SS component -3.02   3.45
pWR501_0148 mxiJ T3SS component -3.06 2.17 4.33
pWR501_0031   hypothetical protein -3.14   
pWR501_0005   hypothetical protein -3.14   2.49
pWR501_0292 sopA VirG-specific protease -3.25   2.49
pWR501_0291   hypothetical protein -3.31   
pWR501_0138 ipgB invasion protein -3.34   3.66
pWR501_0157 spa15 chaperon -3.34 3.52 4.43
pWR501_0012 shET2-2 enterotoxin -3.38   3.41
pWR501_0156 mxiA T3SS component -3.44   4.67
pWR501_0160 spa32 invasion protein -3.45 1.34 4.63
pWR501_0141   hypothetical protein -3.50   3.71
pWR501_0004 phoN2 apyrase -3.52 2.38 3.25
pWR501_0150 mxiL hypothetical protein -3.59 2.07 4.64
pWR501_0132 acp hypothetical protein -3.62   5.19
pWR501_0166 spa-orf10 hypothetical protein -3.64 1.97 4.52
pWR501_0158 spa47 T3SS component -3.65 3.19 4.69
pWR501_0140 icsB T3SS effector -3.65 2.16 4.43
pWR501_0162 spa24 T3SS component -3.70 2.28 3.71
pWR501_0159 spa13 T3SS component -3.75   5.13
pWR501_0161 spa33 T3SS component -3.75 1.99 4.03
pWR501_0151 mxiM T3SS component -3.81 2.40 4.25
pWR501_0155 mxiC T3SS component -3.86 2.43 4.95
pWR501_0290   hypothetical protein -3.86   2.00
pWR501_0030   putative enterotoxin fragment -3.90 2.20 4.54
pWR501_0163 spa9 T3SS component -3.92 1.93 3.56
pWR501_0137 ipgC chaperon -3.93 1.86 4.04
pWR501_0135 ipaC T3SS effector -3.93 2.65 5.01
pWR501_0165 spa40 T3SS component -3.94   4.02
pWR501_0139 ipgA chaperon -3.95 2.45 4.25
pWR501_0153 mxiD T3SS component -3.98 2.33 4.81
pWR501_0152 mxiE transcriptional activator -4.06 2.51 4.48
pWR501_0154 mxiD T3SS component -4.08 2.66 4.54
pWR501_0134 ipaD T3SS effector -4.16 2.99 4.92
pWR501_0167 spa-orf11 hypothetical protein -4.19 2.85 4.07
pWR501_0136 ipaB T3SS effector -4.24 2.97 4.59
pWR501_0133 ipaA T3SS effector -4.24 3.09 4.98
pWR501_0003   hypothetical protein -4.57   3.29
pWR501_0164 spa29 T3SS component -5.06 2.36 3.32
pWR501_0131 virB transcriptional activator -5.17 2.40 4.26
  1. aS. flexneri 5a str. M90T pWR501 virulence plasmid sequence was used as reference GenBank accession numbers AF348706.
  2. bGenes are arranged in descending order in relation to Log2 of Fold Change values of WT no O2/WT O2 comparison.
  3. cLog2 of Fold Change values of WT no O2/WT O2 and Δfnr no O2/WT no O2 comparisons are presented. Only values considered differentially expressed are shown (p adjust <0.05).