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Table 2 Candidate genes likely to be associated with the VBNC state in Xanthomonas campestris pv. campestris based on RNA-Seq analysis

From: Transcriptional profiling of Xanthomonas campestris pv. campestris in viable but nonculturable state

Classification

Qeury name

Gene name

Log2Fold change

Predicted function

C1/CK

C2/CK

C3/CK

 

Cell motility

XC_RS11405

fliL

-0.75

-1.74

-1.74

flagellar basal body-associated FliL family protein

XC_RS11245

flgB

-0.57

-1.39

-1.31

flagellar basal body rod protein FlgB

XC_RS11270

flgG

-0.90

-1.09

-1.049

flagellar basal-body rod protein FlgG

Stress response

XC_RS16490

clpP

2.42

2.18

1.63

ATP-dependent Clp endopeptidase proteolytic subunit ClpP

XC_RS08995

clpXP

2.32

1.88

1.48

ClpXP protease specificity-enhancing factor

XC_RS16485

clpX

1.85

1.42

0.67

ATP-dependent Clp protease ATP-binding subunit ClpX

XC_RS17810

- a

1.79

1.18

0.73

type II toxin-antitoxin system CcdA family antitoxin

XC_RS05365

- a

1.65

1.33

0.94

type II toxin-antitoxin system RelE/ParE family toxin

XC_RS11730

rpfG

1.45

1.23

0.68

two-component system response regulator

Transcription and translation

XC_RS11160

infA

2.32

1.35

0.29

translation initiation factor IF-1

XC_RS08025

infB

2.09

1.53

0.98

translation initiation factor IF-2

XC_RS08265

infC

2.32

1.97

0.57

translation initiation factor IF-3

XC_RS16935

rpoB

2.17

1.65

1.13

DNA-directed RNA polymerase subunit beta

XC_RS09330

dksA

1.59

1.44

0.72

RNA polymerase-binding protein DksA

XC_RS11780

greA

1.88

1.42

0.84

transcription elongation factor GreA

Pathogenicity

XC_RS08195

virB3

2.60

2.38

2.41

VirB3 family type IV secretion system protein

XC_RS08180

virB11

2.17

1.80

1.16

P-type DNA transfer ATPase VirB11

XC_RS01060

secB

1.94

1.89

1.51

protein-export chaperone SecB

Transport and metabolism

XC_RS04900

pyk

1.45

1.15

0.62

pyruvate kinase

XC_RS15295

katG

1.23

1.10

1.14

catalase/peroxidase

XC_RS16265

acpP

3.40

2.39

1.35

acyl carrier protein

XC_RS09690

guaB

1.78

1.43

0.89

IMP dehydrogenase

XC_RS01110

- a

1.67

1.51

0.41

Fic family protein

XC_RS20570

- a

1.74

1.63

1.30

ABC transporter ATP-binding protein

XC_RS18380

- a

2.31

2.03

1.58

ABC transporter permease

  1. CK indicates time zero, while C1-C3 indicate three time points after exposure to copper each associated with a different stage in the establishment of the VBNC state, namely early (1 d) and developing (2 d) stage induction, and the stable VBNC state (10 d), respectively
  2. a indicates no name has been allocated to these genes in the Xanthomonas campestris pv. campestris 8004 genome annotation database
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BMC Genomics

ISSN: 1471-2164

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