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Table 2 SCOTS identified Xenorhabdus koppenhoeferi genes induced upon infection of the white grub Rhizotrogus majalis.

From: Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis

Class

Gene --Possible function

Id/Sim%

Span

E-value

Cell struture

    
 

dacC-Penicillin-binding protein 6 precursor/D-alanyl-D-alanine carboxypeptidase fraction C (Photorhabdus luminescens, plu1573)

65/78

330

9E-35

 

fliM-Flagella MS-ring protein (P. luminescens, plu1941)

90/98

244

7E-32

 

lpsE -Putative LPS biosynthesis protein (P. luminescens, plu4861)

84/86

132

9E-18

 

ompF-Outer membrane protein (Xenorhabdus nematophila, XENPROT)

88/91

227

2E-38

Regulation

    
 

rseA-Sigma E factor negative regulator (Serratia proteamaculans, Spro_3674)

66/80

165

7E-16

 

tilS-Putative cell cycle protein (P. luminescens, plu0689)

62/81

189

4E-14

 

yijC-HTH-type transcriptional repressor (Escherichia coli, EcSMS35_4410)

100/100

129

3E-16

Virulence

    
 

virH-Putative toxin secretion transporter (Vibrio cholerae, VC0395_A1056)

94/98

230

3E-39

 

xhlA-Putative hemolysin protein (X. nematophila, AY640584)

75/86

258

4E-43

 

rtxC-RTX toxin activating protein (Vibrio vulnificus, VVA1030)

77/93

210

5E-23

 

tcaC-Putative insecticidal toxin complex protein (X. nematophila, AJ308438)

90/95

132

9E-21

Stress response

    
 

gor-Glutathione reductase (Yersinia pseudotuberculosis, YPTS_4032)

88/94

182

3E-12

 

msrA-Peptide methionine sulfoxide reductase (Y. pseudotuberculosis, YPTS_0481)

62/79

179

5E-37

 

resP-Putative resistant protein (Enterobacter nickellidurans, AM003901)

86/95

129

1E-15

 

surA-Peptidyl-prolyl cis-trans isomerase (P. luminescens, plu0611)

81/93

182

7E-21

 

uspB-Universal stress protein (P. luminescens, plu0120)

90/100

100

5E-11

 

xkIS-Putative transposase (Nitrosococcus oceani, Noc_1882)

54/66

360

9E-30

 

rep-Putative rep protein (Salmonella enteritidis, SeSA_C0001)

77/80

192

3E-21

 

res-Putative type III restriction enzyme, res subunit (Bacillus coagulans, BcoaDRAFT_2435)

72/87

261

2E-31

 

rpoB-DNA-directed RNA polymerase (Y. pseudotuberculosis, YPTS_0304)

98/100

240

3E-45

 

rrmB-16S ribosomal RNA methyltransferase (P. luminescens, plu4252)

88/94

150

3E-18

Metabolism

    

- Amino acid synthesis

lysC-Aspartate kinase (S. proteamaculans, Spro_4479)

88/93

182

2E-30

- Cofactor biosynthesis

ubiE-Ubiquinone biosynthesis O-methyltransferase (S. proteamaculans, Spro_3270)

100/100

107

8E-17

- Cofactor metabolism

cobJ-Precorrin-3b c17-methyltransferase (Escherichia blattae, REB001118)

83/91

210

2E-27

- Glyoxylate pathway

aceE-Pyruvate dehydrogenase E1 component (P. luminescens, plu3623)

92/96

156

2E-20

 

aceK-Bifunctional isocitrate dehydrogenase kinase/phosphatase protein (P. luminescens, plu4394)

88/95

174

2E-22

 

dld-D-lactate dehydrogenase (P. luminescens, plu2848)

83/92

251

4E-37

- Lipid synthesis

atoB-beta-ketoadipyl CoA thiolase (Escherichia fergusonii, EFER_1599)

100/100

99

2E-05

- Nucleotide synthesis

purF-Amidophosphoribosyltransferase (P. luminescens, plu3167)

97/97

111

7E-13

- Protein degradation

clpP-ATP-dependent Clp protease proteolytic subunit (Y. enterocolitica, YE3134)

76/88

266

6E-45

- Protein folding

trxB-Predicted redox protein, regulator of disulfide bond formation (Yersinia pestis, YP_3227)

88/90

123

2E-12

Nutrition

    

- Ion uptake

znuA-ABC high-affinity zinc uptake transporter, periplasmic binding protein (P. luminescens, plu2115)

81/87

141

2E-13

- Sugar uptake

malF-Maltose ABC transporter, permease protein (P. luminescens, plu0459)

88/93

168

3E-22

Unknown

    
 

xkst1-Hypothetical protein (Ruminococcus gnavus, RUMGNA_01513)

79/87

141

9E-14

 

xkst2-Hypothetical protein (P. luminescens, plu2317)

76/87

162

8E-9

 

xkst3-Hypothetical protein (P. luminescens, plu3301)

84/93

165

4E-20

 

xkst4-No similarity to known genes

   
 

xkst5-No similarity to known genes

   
 

xkst6-No similarity to known genes

   
  1. Underlined genes were also upregulated in Photorhabdus temperata during infection of R. majalis. Other genes were exclusively induced in X. koppenhoeferi and similar sequences of double-underlined genes were absent in the genome of P. temperata.