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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