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Table 1 Substrate-specific proteins

From: Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis

Specificity

Locus

Description in NCBI

Description in KEGG

Vs. Glucose

Log2 (fold change)

FDR-adjusted p value

Xylan

Clocel_0589

Alpha-l-fucosidase

Alpha-l-fucosidase 2

2.67

2.07E−04

Clocel_0590

Xylose isomerase

Xylose isomerase

3.35

1.43E−04

Clocel_0591

Transaldolase

Transaldolase

3.52

1.46E−06

Clocel_0592

Xylulokinase

Xylulokinase

2.85

7.29E−05

Clocel_1085

Dinitrogenase iron–molybdenum cofactor biosynthesis protein

2.32

4.24E−03

Clocel_1151

Methyl-accepting chemotaxis sensory transducer

Methyl-accepting chemotaxis protein

1.96

1.70E−02

Clocel_1430

Glycoside hydrolase family protein

Alpha-d-xyloside xylohydrolase

1.90

9.48E−03

Clocel_2573

Hypothetical protein Clocel_2573

Chemotaxis protein CheX

1.60

3.95E−03

Clocel_2592

Two component transcriptional regulator, AraC family

3.72

1.49E−04

Clocel_2595

Xylan 1,4-beta-xylosidase

Xylan 1,4-beta-xylosidase

4.70

4.53E−06

Clocel_2596

Sugar ABC transporter periplasmic protein

Ribose transport system substrate-binding protein

4.62

1.06E−03

Clocel_2597

Inner-membrane translocator

Ribose transport system permease protein

4.01

7.36E−05

Clocel_2598

ABC transporter

Ribose transport system ATP-binding protein

4.34

1.89E−05

Clocel_2881

PTS system lactose/cellobiose-specific transporter subunit IIB

PTS system, cellobiose-specific IIB component

1.49

1.70E−02

Clocel_2940

Putative phosphate transport regulator

Hypothetical protein

1.44

2.45E−02

Clocel_3175

phoH family protein

phoH-like ATPase

1.64

3.84E−02

Clocel_3761

ATP:guanido phosphotransferase

1.31

1.37E−02

Clocel_3762

UvrB/UvrC protein

1.42

3.45E−02

Clocel_4277

Aldo/keto reductase

1.08

4.66E−02

Galactomannan

Clocel_0034

Glycoside hydrolase family protein

Alpha-d-xyloside xylohydrolase

1.73

1.04E−02

Clocel_0391

Glycosyltransferase

1.83

1.96E−02

Clocel_0684

Thiazole biosynthesis protein ThiH

2-Iminoacetate synthase

1.57

4.69E−03

Clocel_2225

Cobalamin (vitamin B12) biosynthesis CbiX protein

1.39

4.52E−02

Clocel_2259

pfkB domain-containing protein

2-Dehydro-3-deoxygluconokinase

1.31

1.04E−02

Clocel_2697

Sialate O-acetylesterase

Sialate O-acetylesterase

1.69

1.69E−02

Clocel_2800

Alpha-galactosidase

Alpha-galactosidase

2.99

5.49E−05

Clocel_2962

Inosine-5′-monophosphate dehydrogenase

IMP dehydrogenase

1.31

1.96E−02

Clocel_3175

phoH family protein

phoH-like ATPase

1.98

1.14E−02

Clocel_3194

Mannose-6-phosphate isomerase

Mannose-6-phosphate isomerase

3.77

6.86E−05

Clocel_3196

Glycosidase-like protein

Beta-1,4-mannooligosaccharide/beta-1,4-mannosyl-N-acetylglucosamine phosphorylase

2.65

5.29E−03

Clocel_3198

N-acylglucosamine 2-epimerase

Mannobiose 2-epimerase

3.19

2.10E−03

Clocel_3200

Binding-protein-dependent transport system inner membrane protein

Multiple sugar transport system permease protein

4.76

8.61E−04

Clocel_3201

Extracellular solute-binding protein

Raffinose/stachyose/melibiose transport system substrate-binding protein

4.23

5.49E−05

Clocel_3205

Glycoside hydrolase family 2

Beta-mannosidase

2.55

1.51E−03

Clocel_3657

Xylan 1,4-beta-xylosidase

Xylan 1,4-beta-xylosidase/alpha-N-arabinofuranosidase

1.79

4.26E−02

Clocel_3857

ABC transporter

Multiple sugar transport system ATP-binding protein

2.15

1.03E−03

Clocel_4053

LPXTG-motif cell wall anchor domain-containing protein

Sialate O-acetylesterase

2.28

3.79E−02

Clocel_4087

Aldose 1-epimerase

Aldose 1-epimerase

1.45

2.68E−02

Clocel_4088

Galactose-1-phosphate uridylyltransferase

UDP-glucose–hexose-1-phosphate uridylyltransferase

3.38

1.83E−04

Clocel_4089

UDP-glucose 4-epimerase

UDP-glucose 4-epimerase

2.09

1.82E−03

Clocel_4277

Aldo/keto reductase

1.08

4.26E−02

Pectin

Clocel_0048

Transcriptional regulator, AbrB family

Transcriptional pleiotropic regulator of transition state genes

1.91

2.50E−03

Clocel_0322

tatD family hydrolase

tatD DNase family protein

1.74

8.66E−03

Clocel_0513

Extracellular solute-binding protein

Raffinose/stachyose/melibiose transport system substrate-binding protein

2.12

2.50E−03

Clocel_0519

Glycogen/starch/alpha-glucan phosphorylase

Starch phosphorylase

1.88

1.37E−02

Clocel_1243

Extracellular solute-binding protein

Multiple sugar transport system substrate-binding protein

2.53

9.20E−05

Clocel_1892

Acetate kinase

Acetate kinase

1.31

6.43E−03

Clocel_2210

Nicotinate-nucleotide–dimethyl-benzimidazole phosphoribosyltransferase

Nicotinate-nucleotide–dimethyl-benzimidazole phosphoribosyltransferase

1.08

1.47E−02

Clocel_2214

ATP:corrinoid adenosyltransferase

BtuR/CobO/CobP

Coblalamin adenosyltransferase

1.37

4.25E−02

Clocel_2222

Precorrin-3B C(17)-methyltransferase

Precorrin-3B C17-methyltransferase

1.70

6.63E−03

Clocel_2225

Cobalamin (vitamin B12) biosynthesis CbiX protein

1.95

4.32E−03

Clocel_2227

Precorrin-4 C(11)-methyltransferase

Precorrin-4/cobalt-precorrin-4 C11-methyltransferase

2.11

7.92E−03

Clocel_2250

Altronate dehydratase

Altronate hydrolase

4.07

1.02E−05

Clocel_2251

Mannitol dehydrogenase domain-containing protein

Tagaturonate reductase

4.50

4.39E−06

Clocel_2253

Crp family transcriptional regulator

2.37

2.50E−03

Clocel_2254

Glycoside hydrolase family protein

4.36

4.39E−06

Clocel_2255

Major facilitator superfamily protein

Oligogalacturonide transporter

4.33

4.02E−05

Clocel_2256

Glycosyl hydrolase family protein

Unsaturated rhamnogalacturonyl hydrolase

4.19

1.49E−05

Clocel_2259

pfkB domain-containing protein

2-Dehydro-3-deoxygluconokinase

3.75

1.49E−06

Clocel_2262

Short-chain dehydrogenase/reductase SDR

Gluconate 5-dehydrogenase

3.21

2.11E−02

Clocel_2263

4-Deoxy-l-threo-5-hexosulose-uronate ketol-isomerase

4-Deoxy-l-threo-5-hexosulose-uronate ketol-isomerase

3.15

4.92E−03

Clocel_2403

Glucosamine/fructose-6-phosphate aminotransferase

Glucosamine–fructose-6-phosphate aminotransferase (isomerizing)

1.45

4.57E−03

Clocel_2737

Small GTP-binding protein

1.10

2.98E−02

Clocel_3380

LPXTG-motif cell wall anchor domain-containing protein

4.03

1.27E−04

Clocel_3909

Quorum-sensing autoinducer 2 (AI-2), LuxS

S-ribosylhomocysteine lyase

1.19

2.34E−02

Clocel_4088

Galactose-1-phosphate uridylyltransferase

UDP-glucose–hexose-1-phosphate uridylyltransferase

1.62

1.73E−02

Clocel_4277

Aldo/keto reductase

1.31

8.08E−03

  1. To standardize data, obtained data were normalized with the median for all identified quantitative data. P values were adjusted with the Benjamini–Hochberg method to avoid the problem of multiple testing. For thresholds, we adopted an FDR-adjusted p value of <0.05 and fold change of protein ratio >2.0, compared to glucose.