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Table 4 Major groups of B. cenocepacia genes with altered gene expression in sputum

From: Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepaciagrows in cystic fibrosis sputum

Gene number:

Fold change in expression

Putative gene function:

Antimicrobial resistance

upregulated

  

BCAL1675

2.67

multidrug efflux system transporter protein AmrB

BCAM0200

2.20

efflux system transport protein

BCAM0791

2.11

Major Facilitator Superfamily protein

BCAM0792

2.45

efflux system transport protein

BCAM1362

2.06

putative penicillin-binding protein

BCAM1947

3.76

putative quinoxaline efflux system transport protein

BCAS0034

19.84

metallo-beta-lactamase superfamily protein

downregulated

BCAL0704

2.61

D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein precursor)

BCAL1510

2.72

putative multidrug resistance transporter protein

BCAL1813

2.37

multidrug efflux system outer membrane protein

BCAL2832

2.07

D-alanyl-D-alanine carboxypeptidase/endopeptidase (penicillin-binding protein precursor)

BCAL3511

2.08

multidrug resistance transporter protein

BCAL3514

2.11

outer membrane efflux protein

BCAS0015

2.09

efflux system transport protein

Iron uptake & metabolism

upregulated

BCAL0270

35.59

ferric reductase-like transmembrane component

BCAL0273

8.23

protein CyaY

BCAM2231

2.86

transcriptional regulator PchR

BCAM2232

2.11

putative pyochelin biosynthetic protein PchD

downregulated

BCAL2812

2.59

putative Fur family transcriptional regulator

BCAL3201

2.59

putative TolR-related protein

BCAL3203

2.18

putative periplasmic TolB protein

BCAL3204

2.67

putative OmpA family lipoprotein

Protection against reactive oxygen and nitrogen species

upregulated

BCAL1766

2.23

OsmC-like protein

BCAM1676

19.99

putative nitrite/sulfite reductase

BCAM1677

26.75

conserved hypothetical protein

BCAM2753

8.00

putative organic hydroperoxide resistance protein, ohr gene

Downregulated (none)

Motility and adherence

upregulated

BCAL0124

2.02

flagellar regulon master regulator subunit FlhD

BCAL0525

2.17

flagellar M-ring protein FliF

BCAL0527

2.34

flagellar protein FliS

BCAL3506

2.58

flagellar motor switch protein FliM

BCAM0987

2.69

flagellar hook protein 2 FlgE2

BCAM2143

2.33

cable pilus associated adhesin protein

BCAS0299

3.55

flp type pilus subunit

downregulated

BCAL3504

3.31

flagellar protein FliO

BCAM2758

2.35

two-component regulatory system, sensor kinase protein

BCAM2759

3.73

putative minor pilin and initiator

BCAM2761

2.53

giant cable pilus

BCAM2762

2.81

giant cable pilus chaperone protein

BCAS0301

2.03

putative flp type pilus leader peptidase

Secretion

upregulated

BCAL0849

3.39

metallo peptidase, subfamily M48B

BCAL3517

2.36

type II secretion system protein L

BCAM2040

2.98

type III secretion system protein

BCAM2042

2.16

type III secretion system protein

BCAS0196

3.25

putative polygalacturonase

BCAS0409

6.36

zinc metalloprotease ZmpA

downregulated

BCAL3515

2.62

type II secretion system protein N

BCAL3521

3.19

type II secretion system protein I

BCAL3522

2.21

type II secretion system protein H

BCAM0240

2.47

N-acylhomoserine lactone dependent regulatory protein

Selected gene clusters

upregulated

  

BCAL0269

20.82

putative oxidoreductase

BCAL0270

35.59

ferric reductase-like transmembrane component

BCAL1106

90.32

cytochrome b561 family protein

BCAL1107

65.79

putative oxidoreductase

BCAL1153

3.30

putative salicylaldehyde/benzaldehyde dehydrogenase

BCAL1156

2.02

putative 4-hydroxybenzoate transporter

BCAL1157

2.51

putative monooxygenase

BCAM1676

19.99

putative nitrite/sulfite reductase

BCAM1677

26.75

conserved hypothetical protein

BCAM2749

31.39

carboxymuconolactone decarboxylase family protein

BCAM2750

14.06

putative exported protein

BCAM2751

7.13

LysR family regulatory protein

BCAM2752

12.35

NAD dependent epimerase/dehydratase family protein

BCAM2753

8.00

putative organic hydroperoxide resistance protein

BCAM2754

10.46

putative ketoreductase

downregulated

BCAL1130

2.10

conserved hypothetical protein

BCAL1161

2.46

conserved hypothetical protein

BCAL1162

2.30

TetR family regulatory protein

BCAL1165

5.59

conserved hypothetical protein

BCAL1166

4.07

conserved hypothetical protein

BCAL1168

3.06

conserved hypothetical protein

BCAL1169

2.05

conserved hypothetical protein (pseudogene)

BCAL3104

8.00

urease gamma subunit

BCAL3105

2.22

urease beta subunit

BCAL3106

2.34

urease alpha subunit

BCAL3109

2.42

urease accessory protein

BCAM0066

5.13

putative lipoprotein

BCAM0067

14.47

putative short chain dehydrogenase

BCAM0068

11.74

Major Facilitator Superfamily protein

BCAM0069

21.83

conserved hypothetical protein

BCAM0070

15.46

putative hydrolase

BCAM0071

11.11

puatative mandelate racemase lactonizing enzyme

BCAM0072

16.58

putative thiamine pyrophosphate enzyme

BCAM0073

6.85

hypothetical protein

BCAM0074

9.43

conserved hypothetical protein