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Table 1 Proteins Predicted to be up- or downregulated, by Protein Pilot, with p values ≤ 0.05

From: Comparative analyses of proteins from Haemophilus influenzae biofilm and planktonic populations using metabolic labeling and mass spectrometry

 

1Biofilm: Planktonic ratio

 

Accession #

Protein name

Rep. 1

Rep. 2

Rep. 3

2Localization

Amino acid biosynthesis

    

AAX87912.1

glutamine synthetase, GlnA

1.71

 

1.88

Cytoplasmic

AAX87713.1

ketol-acid reductoisomerase, IlvC

  

1.26

Cytoplasmic

AAX87519.1

D-3-phosphoglycerate dehydrogenase, SerA

  

0.54

Cytoplasmic

AAX87314.1

dihydrodipicolinate synthase, DapA

0.66

  

Cytoplasmic

Biosynthesis of cofactors, prosthetic groups, and carriers

   

AAX87263.1

NAD nucleotidase, NadN

2.47

1.62

1.23

Periplasmic

AAX87920.1

octaprenyl-diphosphate synthase, IspB

  

0.71

Cytoplasmic

AAX87900.1

putative heme iron utilization protein

  

0.82

Cytoplasmic

Cell envelope

    

AAX88031.1

transferrin-binding protein 1, Tbp1

1.86

  

OMP

AAX87746.1

VacJ lipoprotein

1.58

  

OMP

AAX87040.1

rod shape-determining protein MreB

1.41

  

Cytoplasmic

AAX88649.1

acylneuraminate cytidylyltransferase, SiaB

  

0.70

Cytoplasmic

AAX88164.1

Outer membrane protein P5

 

0.58

 

OMP

Cellular processes

    

AAX88712.1

predicted periplasmic or secreted lipoprotein

1.57

  

Periplasmic

AAX87955.1

protective surface antigen D15

1.44

  

OMP

AAX88561.1

cell division protein MukB

1.18

  

Unknown

AAX88143.1

cell division protein FtsA

 

0.76

 

Cytoplasmic

AAX87967.1

catalase, HktE

0.76

  

Periplasmic

Central intermediary metabolism

    

AAX87206.1

putative sialic acid transporter, TRAP-type C4-dicarboxylate transport system, periplasmic component, SiaP

0.67

 

0.63

Periplasmic

DNA metabolism

    

AAX87735.1

DNA mismatch repair protein MutS

2.91

  

Cytoplasmic

AAX88107.1

DNA ligase, LigN

 

2.26

 

Cytoplasmic

AAX88664.1

transcription-repair coupling factor, Mfd

1.48

  

Cytoplasmic

AAX88280.1

DNA-binding protein H-NS homolog

1.40

  

Cytoplasmic

AAX88572.1

DNA topoisomerase I, TopA

1.38

  

Cytoplasmic

AAX87482.1

DNA-binding protein HU

  

1.31

Cytoplasmic

AAX87308.1

UvrABC system protein A

 

1.28

 

Cytoplasmic

AAX88029.1

DNA polymerase III, beta chain, DnaN

  

0.81

Cytoplasmic

Energy metabolism

    

AAX87718.1

glycerophosphoryl diester phosphodiesterase precursor, Glp

1.51

 

1.89

Unknown

AAX88650.1

putative NAD(P)H nitroreductase, NsfB

 

1.80

 

Unknown

AAX87025.1

citrate lyase alpha chain, citF

1.38

 

1.71

Cytoplasmic

AAX88575.1

NAD(P) transhydrogenase subunit alpha, PntA

1.43

 

1.62

Cyto. Memb.

AAX88675.1

NADP-dependent malic enzyme, Mao2

1.56

  

Cytoplasmic

AAX88704.1

D-lactate dehydrogenase, Dld

1.26

  

Cyto. Memb.

AAX88019.1

6-phosphofructokinase, PfkA

  

0.52

Cytoplasmic

AAX87882.1

fumarate reductase flavoprotein subunit, FrdA

 

0.54

 

Cyto. Memb.

AAX88128.1

transaldolase, TalB

  

0.55

Unknown

AAX87573.1

fructose-bisphosphate aldolase, Fba

0.73

 

0.55

Cytoplasmic

AAX88202.1

acetate kinase, AckA

0.70

 

0.55

Cytoplasmic

AAX88159.1

thioredoxin reductase, TrxB

  

0.56

Cytoplasmic

AAX87856.1

phosphoenolpyruvate carboxykinase, PckA

  

0.57

Cytoplasmic

AAX88535.1

fumarate hydratase class II, FumC

  

0.59

Cytoplasmic

AAX87709.1

triosephosphate isomerase, TpiA

  

0.64

Cytoplasmic

AAX88580.1

1,4-alpha-glucan branching enzyme, GlgB

  

0.66

Cytoplasmic

AAX88208.1

malate dehydrogenase, Mdh

0.66

  

Unknown

AAX87248.1

flavodoxin, FldA

0.68

  

Cytoplasmic

AAX87583.1

aspartate ammonia-lyase, AspA

  

0.70

Cytoplasmic

AAX87004.1

glyceraldehyde 3-phosphate dehydrogenase, GapA

0.70

0.78

Cytoplasmic

AAX88293.1

pyruvate kinase, PykA

  

0.72

Cytoplasmic

AAX87574.1

phosphoglycerate kinase, Pgk

0.75

  

Cytoplasmic

AAX87971.1

enolase, Eno

0.77

 

0.81

Cytoplasmic

AAX88160.1

thioredoxin domain-containing protein, YbbN

  

0.78

Cytoplasmic

AAX87237.1

formate acetyltransferase, PflB

  

0.79

Cytoplasmic

Fatty acid and phospholipid metabolism

    

AAX87797.1

glycerol-3-phosphate acyltransferase, PlsB

1.50

  

Cyto. Memb.

AAX87445.1

long-chain-fatty-acid--CoA ligase, LcfA

1.60

  

Cyto. Memb.

AAX88571.1

probable acyl carrier protein phosphodiesterase, AcpD

1.50

  

Cytoplasmic

Hypothetical proteins

    

AAX87451.1

conserved hypothetical cupin superfamily metalloenzyme

 

1.36

 

Cytoplasmic

AAX88259.1

conserved hypothetical phosphate transport regulator

  

0.65

Cytoplasmic

AAX87425.1

conserved hypothetical protein

 

0.73

 

Unknown

AAX88050.1

conserved hypothetical protein

0.80

  

Cytoplasmic

Protein fate

     

AAX87914.1

peptidase B, pepB

  

1.52

Cytoplasmic

AAX87592.1

60 kDa chaperonin, GroEL

  

1.52

Cytoplasmic

AAX87863.1

Xaa-Pro aminopeptidase, PepP

  

1.51

Cytoplasmic

AAX88683.1

chaperone protein DnaK

  

1.42

Cytoplasmic

AAX87793.1

protein-export protein SecB

 

1.41

 

Cytoplasmic

AAX87272.1

oligopeptidase A, PrlC

1.37

1.28

 

Cytoplasmic

AAX87706.1

aminoacyl-histidine dipeptidase, PepD

1.32

  

Cytoplasmic

AAX87591.1

10 kDa chaperonin, GroES

0.42

  

Cytoplasmic

AAX87652.1

peptidase E, PepE

0.52

  

Cytoplasmic

AAX87816.1

cell division protein FtsY

  

0.56

Cytoplasmic

AAX88211.1

thiol:disulfide interchange protein DsbC

0.58

  

Periplasmic

AAX87741.1

trigger factor, Tig

  

0.64

Cytoplasmic

AAX88760.1

cytosol aminopeptidase, PepA

  

0.72

Cytoplasmic

Protein synthesis

    

AAX88424.1

phenylalanyl-tRNA synthetase beta chain, PheT

  

2.11

Cytoplasmic

AAX87782.1

prolyl-tRNA synthetase, ProS

  

2.00

Cytoplasmic

AAX87660.1

30S ribosomal protein S7, RpsG

  

1.81

Cytoplasmic

AAX87825.1

50S ribosomal protein L3, RplC

  

1.53

Cytoplasmic

AAX87593.1

50S ribosomal protein L9, RplI

 

1.31

 

Cytoplasmic

AAX88652.1

methionyl-tRNA synthetase, MetG

 

1.29

 

Cytoplasmic

AAX87177.1

Seryl-tRNA synthetase, SerS

 

1.25

 

Cytoplasmic

AAX87580.1

30S ribosomal protein S21, RpsU

0.49

  

Cytoplasmic

AAX87839.1

30S ribosomal protein S14, RpsN

0.47

  

Cytoplasmic

AAX87952.1

elongation factor Ts

0.59

 

0.58

Cytoplasmic

AAX87661.1

elongation factor G, FusA

0.61

 

0.76

Cytoplasmic

AAX87855.1

ribosome recycling factor, Frr

0.68

0.73

0.62

Cytoplasmic

AAX87080.1

cysteinyl-tRNA synthetase, CysS

0.62

  

Cytoplasmic

AAX88252.1

tyrosyl-tRNA synthetase, TyrS

  

0.63

Cytoplasmic

AAX87851.1

50S ribosomal protein L17, RplQ

0.66

  

Cytoplasmic

AAX87670.1

50S ribosomal protein L10, RplJ

0.67

  

Cytoplasmic

AAX87910.1

GTP-binding protein TypA/ BipA

  

0.68

Cyto. Memb.

AAX87836.1

50S ribosomal protein L14, RplN

 

0.71

 

Cytoplasmic

AAX87838.1

50S ribosomal protein L5, RplN

0.74

  

Cytoplasmic

AAX88285.1

arginyl-tRNA synthetase, ArgS

0.74

  

Cytoplasmic

AAX87448.1

predicted GTPase, probable translation factor

  

0.74

Cytoplasmic

AAX87662.1

elongation factor Tu, TufB

 

0.80

0.81

Cytoplasmic

AAX88543.1

valyl-tRNA synthetase, ValS

  

0.83

Cytoplasmic

AAX87376.1

aspartyl-tRNA synthetase, AspS

  

0.85

Cytoplasmic

Purines, pyrimidines, nucleosides, and nucleotides processes

    

AAX87406.1

adenylate kinase, Adk

0.55

 

0.66

Cytoplasmic

AAX88253.1

Ribose-phosphate pyrophosphokinase, PrsA

0.57

 

0.80

Cytoplasmic

AAX87655.1

2’,3’-cyclic-nucleotide 2’-phosphodiesterase, CpdB

0.78

 

0.61

Periplasmic

AAX88085.1

CTP synthase, PyrG

 

0.62

 

Cytoplasmic

AAX87567.1

Purine nucleoside phosphorylase, DeoD

  

0.65

Cytoplasmic

AAX87928.1

Serine hydroxymethyltransferase, GlyA

0.75

  

Cytoplasmic

Regulatory functions

    

AAX87211.1

HflK

1.36

  

Cytoplasmic

AAX87210.1

HflC

1.22

  

Cytoplasmic

AAX87923.1

aerobic respiration control protein ArcA

0.37

 

0.35

Cytoplasmic

Transcription

    

AAX88453.1

transcription elongation factor GreA

1.60

  

Cytoplasmic

AAX88611.1

transcription elongation protein NusA

  

1.44

Cytoplasmic

AAX87564.1

DNA-directed RNA polymerase beta chain, RpoB

1.17

 

1.32

Cytoplasmic

AAX87290.1

polyribonucleotide nucleotidyltransferase, Pnp

1.17

 

1.18

Cytoplasmic

AAX87467.1

ribonuclease E, Rne

  

1.14

Cytoplasmic

AAX87292.1

Cold-shock DEAD-box protein A homolog, DeaD

0.52

 

Cytoplasmic

Transport and binding proteins

    

AAX88593.1

spermidine/putrescine-binding periplasmic protein 1 precursor, PotD1

  

2.04

Periplasmic

AAX88216.1

putative L-lactate permease

1.96

 

1.68

Cyto. Memb.

AAX87899.1

heme-binding protein A, HbpA

1.73

  

Periplasmic

AAX87717.1

glycerol-3-phosphate transporter, GlpT

1.50

  

Cyto. Memb.

AAX87322.1

heme/hemopexin-binding protein B, HxuB

1.45

  

OMP

AAX88215.1

heme utilization protein, Hup

1.37

  

OMP

AAX88590.1

spermidine/putrescine transport ATP-binding protein, PotA

 

1.34

 

Cyto. Memb.

AAX87417.1

putative periplasmic chelated iron binding protein, HfeA

1.31

  

Periplasmic

AAX88729.1

predicted regulator of cell morphogenesis and NO signaling

0.77

 

0.39

Cytoplasmic

AAX88749.1

molybdate-binding periplasmic protein, ModA

0.46

0.69

 

Periplasmic

AAX87869.1

D-galactose-binding periplasmic protein precursor, MglB

0.64

 

0.59

Periplasmic

AAX88127.1

periplasmic oligopeptide-binding protein, OppA

0.71

 

0.61

Periplasmic

AAX87555.1

Ribose-binding periplasmic protein, RbsB

 

0.68

 

Periplasmic

AAX88552.1

phosphate-binding periplasmic protein precursor PstS

0.72

 

0.70

Periplasmic

AAX88551.1

ferritin like protein 1, FtnA

0.77

  

Cytoplasmic

AAX87184.1

high-affinity zinc uptake system protein ZnuA

0.77

  

Periplasmic

AAX87223.1

Na(+)-translocating NADH-quinone reductase subunit A, NqrA

 

0.84

 

Cytoplasmic

  1. 1Bolded ratios show proteins predicted to be upregulated in the biofilm. Non-bolded ratios are proteins predicted to be downregulated in the biofilm.
  2. 2Localization determined using PSORTb program. OMP = outer membrane protein, Cyto. Memb. = cytoplasmic membrane protein.