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Table 2 Genes with increased expression in either the bprR and/or bprS single mutants

From: Perturbation of the two-component signal transduction system, BprRS, results in attenuated virulence and motility defects in Burkholderia pseudomallei

Locus tag

Gene name

Description

bprS mutant Expression (log2)

bprS mutant FDR

bprR mutant Expression (log2)

bprR mutant FDR

BPSL0026

fliL

flagellar basal body-associated protein FliL

2.09

8.28E-03

1.82#

1.52E-02

BPSL0028

fliN

flagellar motor switch protein

2.25

5.34E-03

1.94

9.47E-03

BPSL0031

fliQ

flagellar biosynthesis protein

2.15

5.34E-03

1.93#

1.08E-02

BPSL0067

 

protein of unknown function

2.54

2.16E-05

2.30

2.20E-05

BPSL0068

 

putative lipoprotein

2.46

2.16E-05

2.30

2.11E-05

BPSL0069

 

putative anti-sigma factor

1.02

4.78E-03

0.89

1.09E-02

BPSL0071

 

putative catalase

1.31

4.26E-03

1.47

2.44E-03

BPSL0225

 

putative flagellar hook-length control protein

1.76

1.24E-03

1.24

6.62E-03

BPSL0226

fliJ

flagellar fliJ protein

1.87

1.75E-03

1.34#

1.09E-02

BPSL0227

fliI

flagellum-specific ATP synthase

1.94

5.34E-03

1.54#

1.32E-02

BPSL0228

fliH

flagellar assembly protein H

2.04

8.43E-03

1.69#

1.69E-02

BPSL0230

fliF

flagellar MS-ring protein

2.14

8.20E-03

1.75#

1.64E-02

BPSL0231

fliE

flagellar hook-basal body complex protein

1.81

8.84E-03

1.39#

2.52E-02

BPSL0269

flgA

flagellar basal body P-ring biosynthesis protein FlgA

2.09

2.38E-03

1.58#

1.08E-02

BPSL0271

flgC

flagellar basal body rod protein FlgC

2.20

6.66E-03

1.75#

1.52E-02

BPSL0272

flgD

flagellar basal body rod modification protein

2.12

7.33E-03

1.76#

1.43E-02

BPSL0273

flgE

flagellar hook protein FlgE

1.88

3.02E-03

1.39#

1.22E-02

BPSL0274

flgF

flagellar basal body rod protein FlgF

1.79

4.69E-03

1.29#

1.66E-02

BPSL0275

flgG

flagellar basal body rod protein FlgG

1.92

5.66E-03

1.43#

1.64E-02

BPSL0276

flgH

flagellar basal body L-ring protein

1.88

2.96E-03

1.44#

1.03E-02

BPSL0278

flgJ

flagellar rod assembly protein/muramidase FlgJ

1.83

4.51E-03

1.27#

1.87E-02

BPSL0403

 

mce related protein

1.19

1.26E-03

1.22

7.78E-04

BPSL0812

bpeR

TetR family regulatory protein

1.09

7.33E-03

1.08

8.20E-03

BPSL0814

bpeA

RND family acriflavine resistance protein A precursor

1.65

2.23E-03

1.56

2.22E-03

BPSL0815

bpeB

RND family acriflavine resistance protein

1.84

7.63E-03

1.79

7.22E-03

BPSL1053

 

putative lipoprotein

0.48

3.05E-01

1.50

5.74E-03

BPSL1112

 

putative lipoprotein

1.54

1.55E-03

1.24

6.71E-03

BPSL1184

 

putative sugar-related transport, membrane protein

1.01

6.70E-03

0.88

1.37E-02

BPSL1185

 

protein of unknown function

3.95

3.83E-05

4.04

2.11E-05

BPSL1202

 

putative transport-related membrane protein

0.61

8.41E-02

1.93

2.32E-04

BPSL1203

 

putative carbonic anhydrase

0.63

6.17E-02

2.03

9.28E-05

BPSL1254

 

protein of unknown function

1.59

4.26E-03

1.75

2.10E-03

BPSL1289

osmB

osmotically inducible lipoprotein B precursor

0.72

3.89E-02

1.66

2.80E-04

BPSL1387

 

protein of unknown function

1.09

1.34E-03

0.77

8.20E-03

BPSL1563

 

putative membrane protein of unknown function

1.22

5.17E-04

1.68

4.16E-05

BPSL1564

 

putative transcriptional regulatory protein

0.50

1.17E-01

1.37

9.39E-04

BPSL1598

 

putative transport-related, membrane protein

0.28

3.17E-01

1.59

1.66E-04

BPSL1829

 

putative methyl-accepting chemotaxis protein

1.98

4.26E-03

1.34#

1.89E-02

BPSL1872

 

putative N-acetylmuramoyl-L-alanine amidase

1.07#

3.99E-02

1.47

9.64E-03

BPSL1931

 

protein of unknown function

0.83

2.35E-02

1.01

9.10E-03

BPSL2011

 

putative osmosis-related lipoprotein

−0.35

2.54E-01

1.08

2.78E-03

BPSL2016

 

protein of unknown function

0.78

5.21E-02

1.30

5.35E-03

BPSL2017

 

di-haem cytochrome c peroxidase

0.67

1.09E-01

1.38

5.35E-03

BPSL2193

 

protein of unknown function

0.90

7.52E-03

1.12

2.10E-03

BPSL2282

 

protein of unknown function

0.62

6.86E-02

1.97

1.20E-04

BPSL2396

 

protein of unknown function

1.27

7.30E-03

1.30

5.74E-03

BPSL2397

 

protein of unknown function

1.46

2.48E-03

1.25

5.30E-03

BPSL2398

 

protein of unknown function

1.12#

1.09E-02

1.18

7.39E-03

BPSL2399

 

putative glycosyltransferase

1.36

1.55E-03

1.19

2.72E-03

BPSL2409

 

ABC transporter ATP binding protein

0.85

2.82E-02

1.09

8.00E-03

BPSL2466

 

protein of unknown function

0.76

1.43E-02

2.03

2.30E-05

BPSL2482

 

peptidase

1.25

2.38E-03

1.32

1.27E-03

BPSL2483

 

ribosome-associated GTPase

0.97

5.86E-03

1.01

4.35E-03

BPSL3254B

 

protein of unknown function

1.63

1.22E-03

1.94

2.75E-04

BPSL3291

fliA

flagellar biosynthesis sigma factor

1.86

2.45E-03

1.50

6.41E-03

BPSL3292

flhG

flagellar biosynthesis protein FlhG

2.21

3.79E-03

1.74#

1.08E-02

BPSL3293

flhF

flagellar biosynthesis regulator FlhF

2.23

1.83E-03

1.75

5.35E-03

BPSL3294

flhA

flagellar biosynthesis protein FlhA

2.09

7.89E-03

1.67#

1.66E-02

BPSL3323

 

putative transferase

1.55

8.43E-03

1.13#

2.51E-02

BPSL3324

 

putative keto/oxo acyl-ACP synthase

1.51

7.17E-03

0.98

3.22E-02

BPSL3326

 

putative keto/oxo acyl-ACP synthase

1.78

8.43E-03

1.39#

1.99E-02

BPSL3327

 

putative short chain dehydrogenase

1.74

3.62E-03

1.26#

1.52E-02

BPSL3329

 

Rieske (2Fe-2S) domain-containing protein

1.31

7.21E-03

0.95

2.29E-02

BPSS0215

tar

methyl-accepting chemotaxis protein

1.70

6.71E-03

1.35#

1.58E-02

BPSS0216

 

putative membrane protein of unknown function

1.12

4.45E-03

0.82

1.97E-02

BPSS0223

 

protein of unknown function

0.82

8.44E-03

1.44

2.34E-04

BPSS0236

ltaE

L-allo-threonine aldolase

0.96

2.09E-02

1.20

6.20E-03

BPSS0264

 

protein of unknown function

1.02#

2.56E-02

1.36

6.20E-03

BPSS0298

 

transport related membrane protein

1.60

1.36E-03

1.07#

1.37E-02

BPSS0299

malM

fatty-acid CoA ligase

2.20

8.23E-03

1.63#

2.27E-02

BPSS0300

malL

malonyl CoA-acyl carrier protein

2.29

2.38E-03

1.60#

1.17E-02

BPSS0301

malK

protein of unknown function

2.24

1.91E-03

1.60

9.10E-03

BPSS0302

malJ

fatty acid biosynthesis-related CoA ligase

2.30

2.96E-03

1.66#

1.29E-02

BPSS0303

malI

diaminopimelate decarboxylase

2.39

8.17E-04

1.81

2.78E-03

BPSS0304

malH

protein of unknown function

2.60

3.60E-04

1.93

1.38E-03

BPSS0305

malG

ketol-acid reductoisomerase

2.51

3.20E-04

1.95

9.39E-04

BPSS0306

malF

multifunctional polyketide-peptide syntase

2.67

5.32E-04

2.14

1.38E-03

BPSS0307

malE

gamma-aminobutyraldehyde dehydrogenase

2.81

1.53E-04

2.35

2.60E-04

BPSS0308

malD

protein of unknown function

2.75

1.55E-04

2.23

3.46E-04

BPSS0309

malC

peptide synthase regulatory protein

2.89

8.78E-05

2.33

2.10E-04

BPSS0310

malB

protein of unknown function

2.98

1.53E-04

2.62

2.20E-04

BPSS0311

malA

multifunctional polyketide-peptide syntase

3.10

5.17E-04

2.87

4.96E-04

BPSS0312

malR

LuxR family transcriptional regulator

1.47

6.27E-04

1.12

2.72E-03

BPSS0317

 

monooxygenase

1.54

1.55E-03

2.38

6.99E-05

BPSS0325

 

putative membrane protein of unknown function

0.32

2.91E-01

1.07

3.74E-03

BPSS0337

 

protein of unknown function

1.38

1.24E-03

1.91

1.20E-04

BPSS0623

 

outer membrane efflux protein

2.09

5.17E-04

2.27

2.10E-04

BPSS0624

macB

macrolide-specific ABC-type efflux carrier

1.95

1.61E-03

2.22

4.96E-04

BPSS0625

 

drug-efflux protein

1.97

6.27E-04

2.15

2.33E-04

BPSS0685

 

protein of unknown function

1.21

6.63E-04

0.89

5.35E-03

BPSS0686a

 

Predicted 5,10-methylene tetrahydromethanopterin reductase

3.39

1.14E-07

0.35

1.71E-01

BPSS0686aa

 

protein of unknown function

5.16

8.78E-05

−0.47

5.88E-01

BPSS0687 a

 

sensor kinase protein

5.89

7.90E-09

1.46

2.89E-04

BPSS0688 a

 

response regulator protein

4.56

9.34E-09

4.70

7.98E-09

BPSS0689

 

protein of unknown function

7.12

7.90E-09

7.78

5.57E-09

BPSS0690

 

protein of unknown function

6.45

1.06E-08

6.49

9.89E-09

BPSS0692

 

fumarylacetoacetate (FAA) hydrolase family protein

2.26

1.55E-04

2.16

2.10E-04

BPSS0693

 

fumarylacetoacetate (FAA) hydrolase family protein

2.07

1.53E-04

1.88

2.10E-04

BPSS0694

hpcC

5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

2.14

2.48E-05

2.18

1.82E-05

BPSS0695

hpcB

3,4-dihydroxyphenylacetate 2,3-dioxygenase

1.81

8.07E-05

1.84

4.84E-05

BPSS0696

hpcD

5-carboxymethyl-2-hydroxymuconate delta-isomerase

2.19

1.53E-04

1.98

2.44E-04

BPSS0697

hpcG

2-oxo-hepta-3-ene-1,7-dioic acid hydratase

1.85

2.01E-04

1.89

1.69E-04

BPSS0698

hpcH

2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase

2.01

1.55E-04

1.99

1.67E-04

BPSS0724

 

protein of unknown function

0.83

7.33E-03

1.09

1.38E-03

BPSS0755

 

LysR family regulatory protein

0.57

3.11E-02

1.03

1.23E-03

BPSS0796A

 

H-NS-like protein

1.71

2.38E-03

4.39

1.27E-06

BPSS0797

 

IclR family regulatory protein

1.03

6.40E-02

3.95

1.96E-05

BPSS0798

 

protein of unknown function

0.68

1.60E-01

3.35

2.11E-05

BPSS0799

 

diguanylate phosphodiesterase

1.04

9.65E-03

4.48

1.31E-07

BPSS0828

 

protein of unknown function

0.82

3.54E-02

1.21

5.35E-03

BPSS0852

 

inosine-uridine preferring nucleoside hydrolase

1.60

6.57E-03

1.74

3.49E-03

BPSS0941

 

protein of unknown function

1.07

8.73E-03

1.33

2.78E-03

BPSS0946

penA

beta-lactamase precursor

1.94

2.38E-03

2.65

2.44E-04

BPSS1038

 

protein of unknown function

0.04

9.47E-01

1.66

5.01E-03

BPSS1239

 

peptidase

0.33

6.92E-01

2.76

2.53E-03

BPSS1250

 

acetylpolyamine aminohydrolase

0.95

2.14E-02

1.10

9.81E-03

BPSS1275

 

RNA polymerase sigma factor

1.25

7.92E-03

1.51

2.99E-03

BPSS1296

 

O-methyltransferase-like protein

0.88

1.11E-02

1.05

4.84E-03

BPSS1553

bprP

Transcriptional regulator

1.57

2.04E-03

1.19

8.84E-03

BPSS1554

bprQ

Protein associated with bprP

1.43

1.28E-03

1.31

2.27E-03

BPSS1862

 

ABC transport system, ATP-binding protein

1.70

8.43E-03

1.71

7.39E-03

BPSS1866

 

lipoprotein

0.21

5.80E-01

1.44

2.10E-03

BPSS1867

 

protein of unknown function

1.42#

1.21E-02

2.20

9.10E-04

BPSS1980

 

protein of unknown function

0.66

1.61E-02

1.31

2.44E-04

BPSS1996

 

protein of unknown function

1.13

8.44E-02

2.84

8.95E-04

BPSS2162

 

protein of unknown function

0.42

5.50E-01

2.13

6.14E-03

BPSS2307

 

amidase

0.61

1.05E-01

1.47

1.92E-03

BPSS2308

 

protein of unknown function

1.01

1.26E-03

1.97

1.14E-05

  1. Genes were identified as differentially expressed if they showed >2-fold expression change (log2 > 1.0) compared to the wild-type strain with a False Discovery Rate (FDR) of <0.01. All significant gene expression changes are shown in bold and the locus tag, gene name and description are shown in bold when significant expression changes were observed for both mutants
  2. aIncreased RNA expression also observed in the bprRS double mutant (Table 1)
  3. #Genes showing increased expression of >2-fold with a FDR of >0.01 and <0.05