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Table 3 Genes exhibiting the same pattern of change for both deletions under acidogenesis

From: Elucidation of the roles of adhE1 and adhE2 in the primary metabolism of Clostridium acetobutylicum by combining in-frame gene deletion and a quantitative system-scale approach

Locus number

Function

ΔadhE1/Control strain

ΔadhE2/Control strain

Notea

Up-regulation

 CA_C0102

O-acetylhomoserine sulfhydrylase

28.70

20.49

CymR

 CA_C0103

Adenylylsulfate kinase

32.55

22.06

CymR

 CA_C0104

Adenylylsulfate reductase, subunit A

48.44

28.89

CymR

 CA_C0105

Ferredoxin

30.78

21.84

CymR

 CA_C0106

ABC-type probable sulfate transporter, periplasmic binding protein

26.09

14.54

CymR

 CA_C0107

ABC-type sulfate transporter, ATPase component

22.86

13.03

CymR

 CA_C0108

ABC-type probable sulfate transporter, permease protein

35.38

19.05

CymR

 CA_C0109

Sulfate adenylate transferase, CysD subfamily

42.53

26.82

CymR

 CA_C0110

GTPase, sulfate adenylate transferase subunit 1

54.78

42.48

CymR

 CA_C0117

Chemotaxis protein cheY homolog

8.34

6.69

 

 CA_C0118

Chemotaxis protein cheA

11.00

8.24

 

 CA_C0119

Chemotaxis protein cheW

13.83

9.52

 

 CA_C0120

Membrane-associated methyl-accepting chemotaxis protein with HAMP domain

6.93

5.29

 

 CA_C0878

Amino acid ABC transporter permease component

5.61

4.04

CymR

 CA_C0879

ABC-type polar amino acid transport system, ATPase component

8.29

5.60

CymR

 CA_C0880

Periplasmic amino acid binding protein

9.50

6.50

CymR

 CA_C0930

Cystathionine gamma-synthase

4.58

4.72

CymR

 CA_C1392

Glutamine phosphoribosylpyrophosphate amidotransferase

4.20

4.47

 

 CA_C1394

Folate-dependent phosphoribosylglycinamide formyltransferase

4.11

4.57

 

 CA_C2072

Stage IV sporulation protein B, SpoIVB

∞

∞

 

 CA_C2235

Cysteine synthase/cystathionine beta-synthase, CysK

8.27

7.17

CymR

 CA_C2236

Uncharacterized conserved protein of YjeB/RRF2 family

4.29

4.06

CymR encoding gene

 CA_C2241

Cation transport P-type ATPase

7.92

7.62

 

 CA_C2242

Predicted transcriptional regulator, arsE family

5.01

5.22

 

 CA_C2521

Hypothetical protein, CF-41 family

4.33

5.70

 

 CA_C2533

Protein containing ChW-repeats

∞

∞

 

 CA_C2816

Hypothetical protein, CF-17 family

6.00

11.20

 

 CA_C3049

Glycosyltransferase

4.79

7.42

 

 CA_C3050

AMSJ/WSAK-related protein, possibly involved in exopolysaccharide biosynthesis

4.70

8.25

 

 CA_C3051

Glycosyltransferase

5.16

9.60

 

 CA_C3052

Glycosyltransferase

5.59

9.91

 

 CA_C3053

Histidinol phosphatase-related enzyme

7.03

10.94

 

 CA_C3054

Phosphoheptose isomerase

6.69

11.37

 

 CA_C3055

Sugar kinase

5.90

10.87

 

 CA_C3056

Nucleoside-diphosphate-sugar pyrophosphorylase

6.37

11.28

 

 CA_C3057

Glycosyltransferase

12.36

11.92

 

 CA_C3058

Mannose-1-phosphate guanylyltransferase

9.94

11.59

 

 CA_C3059

Sugar transferases

13.47

12.63

 

 CA_C3325

Periplasmic amino acid binding protein

18.24

10.68

CymR

 CA_C3326

Amino acid ABC-type transporter, permease component

19.82

11.79

CymR

 CA_C3327

Amino acid ABC-type transporter, ATPase component

28.33

16.73

CymR

 CA_C3461

Hypothetical protein

4.52

16.79

 

 CA_C3556

Probable S-layer protein;

4.18

10.41

 

 CA_C3636

Oligopeptide ABC transporter, ATPase component

4.23

4.68

 

 CA_P0029

Permease MDR-related

∞

∞

 

 CA_P0030

Isochorismatase

385.91

81.89

 

 CA_P0031

Transcriptional activator HLYU, HTH of ArsR family

46.17

10.93

 

 CA_P0117

Possible beta-xylosidase diverged, family 5/39 of glycosyl hydrolases and alpha-amylase C (Greek key) C-terminal domain

56.53

4.94

 

 CA_P0118

Possible xylan degradation enzyme (glycosyl hydrolase family 30-like domain and Ricin B-like domain)

54.97

5.22

 

 CA_P0119

Possible xylan degradation enzyme (glycosyl hydrolase family 30-like domain and Ricin B-like domain)

46.44

4.23

 

Down-regulation

 CA_C0078

Accessory gene regulator protein B

0.04

0.00

 

 CA_C0079

Hypothetical protein

0.00

0.00

 

 CA_C0082

Predicted membrane protein

0.02

0.00

 

 CA_C0310

Regulators of stationary/sporulation gene expression, abrB B.subtilis ortholog

0.15

0.23

 

 CA_C0381

Methyl-accepting chemotaxis protein

0.18

0.13

 

 CA_C0437

Sensory transduction histidine kinase

0.15

0.23

 

 CA_C0537

Acetylxylan esterase, acyl-CoA esterase or GDSL lipase family, strong similarity to C-terminal region of endoglucanase E precursor

0.15

0.10

 

 CA_C0542

Methyl-accepting chemotaxis protein

0.21

0.08

 

 CA_C0658

Fe-S oxidoreductase

0.24

0.00

 

 CA_C0660

Hypothetical protein, CF-26 family

0.17

0.08

BuOH

 CA_C0814

3-oxoacyl-[acyl-carrier-protein] synthase III

0.11

0.02

BuOH

 CA_C0815

Methyl-accepting chemotaxis protein

0.13

0.04

BuOH

 CA_C0816

Lipase-esterase-related protein

0.17

0.04

BuOH

 CA_C1010

Predicted phosphohydrolase, Icc family

0.21

0.04

BuOH

 CA_C1022

Thioesterase II of alpha/beta hydrolase superfamily

0.22

0.11

 

 CA_C1078

Predicted phosphohydrolase, Icc family

0.17

0.04

BuOH

 CA_C1079

Uncharacterized protein, related to enterotoxins of other Clostridiales

0.15

0.05

 

 CA_C1080

Uncharacterized protein, probably surface-located

0.11

0.01

 

 CA_C1081

Uncharacterized protein, probably surface-located

0.13

0.01

 

 CA_C1532

Protein containing ChW-repeats

0.22

0.08

 

 CA_C1766

Predicted sigma factor

0.19

0.00

 

 CA_C1775

Predicted membrane protein

0.16

0.05

 

 CA_C1868

Uncharacterized secreted protein, homolog YXKC Bacillus subtilis

0.22

0.18

 

 CA_C1989

ABC-type iron (III) transport system, ATPase component

0.18

0.11

BuOH

 CA_C1991

Uncharacterized protein, YIIM family

0.23

0.10

BuOH

 CA_C1993

Molybdenum cofactor biosynthesis enzyme MoaA, Fe-S oxidoreductase

0.23

0.18

BuOH

 CA_C1994

Molybdopterin biosynthesis enzyme, MoaB

0.22

0.11

BuOH

 CA_C1996

Hypothetical protein

0.19

0.08

BuOH

 CA_C1997

Predicted glycosyltransferase

0.19

0.07

BuOH

 CA_C1998

ABC-type transport system, ATPase component

0.19

0.07

BuOH

 CA_C1999

Uncharacterized protein related to hypothetical protein Cj1507c from Campylobacter jejuni

0.20

0.07

BuOH

 CA_C2000

Indolepyruvate ferredoxin oxidoreductase, subunit beta

0.19

0.06

BuOH

 CA_C2001

Indolepyruvate ferredoxin oxidoreductase, subunit alpha

0.13

0.04

BuOH

 CA_C2002

Predicted iron-sulfur flavoprotein

0.16

0.05

BuOH

 CA_C2003

Predicted permease

0.16

0.08

BuOH

 CA_C2004

Siderophore/Surfactin synthetase-related protein

0.10

0.04

BuOH

 CA_C2005

Siderophore/Surfactin synthetase-related protein

0.12

0.05

BuOH

 CA_C2006

Enzyme of siderophore/surfactin biosynthesis

0.15

0.07

BuOH

 CA_C2007

Predicted glycosyltransferase

0.09

0.03

BuOH

 CA_C2008

3-oxoacyl-(acyl-carrier-protein) synthase

0.11

0.04

BuOH

 CA_C2009

3-Hydroxyacyl-CoA dehydrogenase

0.10

0.03

BuOH

 CA_C2010

Predicted Fe-S oxidoreductase

0.09

0.03

BuOH

 CA_C2011

Possible 3-oxoacyl-[acyl-carrier-protein] synthase III

0.12

0.03

BuOH

 CA_C2012

Enoyl-CoA hydratase

0.12

0.04

BuOH

 CA_C2013

Hypothetical protein

0.12

0.03

BuOH

 CA_C2014

Predicted esterase

0.12

0.02

BuOH

 CA_C2015

Hypothetical protein

0.15

0.04

BuOH

 CA_C2016

Enoyl-CoA hydratase

0.12

0.02

BuOH

 CA_C2017

Acyl carrier protein

0.15

0.03

BuOH

 CA_C2018

Aldehyde:ferredoxin oxidoreductase

0.12

0.03

BuOH

 CA_C2019

Malonyl CoA-acyl carrier protein transacylase

0.12

0.02

BuOH

 CA_C2020

Molybdopterin biosynthesis enzyme, MoeA, fused to molybdopterin-binding domain

0.20

0.07

 

 CA_C2021

Molybdopterin biosynthesis enzyme, MoeA (short form)

0.24

0.06

 

 CA_C2023

Membrane protein, related to copy number protein COP from Clostridium perfringens plasmid pIP404 (GI:116,928)

0.22

0.12

 

 CA_C2026

Predicted flavodoxin

0.20

0.09

 

 CA_C2107

Contains cell adhesion domain

0.20

0.08

 

 CA_C2293

Hypothetical secreted protein

0.13

0.10

 

 CA_C2581

6-pyruvoyl-tetrahydropterin synthase-related domain; conserved membrane protein

0.24

0.11

BuOH

 CA_C2663

Protein containing cell wall hydrolase domain

0.23

0.09

 

 CA_C2695

Diverged Metallo-dependent hydrolase(Zn) of DD-Peptidase family; peptodoglycan-binding domain

0.17

0.12

BuOH

 CA_C2807

Endo-1,3(4)-beta-glucanase family 16

0.21

0.02

 

 CA_C2808

Beta-lactamase class C domain (PBPX family) containing protein

0.20

0.04

 

 CA_C2809

Predicted HD superfamily hydrolase

0.14

0.02

 

 CA_C2810

Possible glucoamylase (diverged), 15 family

0.14

0.01

 

 CA_C2944

N-terminal domain intergin-like repeats and c-terminal- cell wall-associated hydrolase domain

0.23

0.06

BuOH

 CA_C3070

Glycosyltransferase

0.21

0.04

 

 CA_C3071

Glycosyltransferase

0.21

0.03

 

 CA_C3072

Mannose-1-phosphate guanylyltransferase

0.18

0.02

 

 CA_C3073

Sugar transferase involved in lipopolysaccharide synthesis

0.23

0.03

 

 CA_C3085

TPR-repeat-containing protein; Cell adhesion domain

0.25

0.12

 

 CA_C3086

Protein containing cell adhesion domain

0.20

0.11

 

 CA_C3251

Sensory transduction protein containing HD_GYP domain

0.20

0.11

 

 CA_C3264

Uncharacterized conserved protein, YTFJ B.subtilis ortholog

0.19

0.15

BuOH

 CA_C3265

Predicted membrane protein

0.08

0.11

 

 CA_C3266

Hypothetical protein

0.07

0.07

 

 CA_C3267

Specialized sigma subunit of RNA polymerase

0.15

0.16

 

 CA_C3280

Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats

0.23

0.14

 

 CA_C3408

NADH oxidase (two distinct flavin oxidoreductase domains)

0.03

0.02

 

 CA_C3409

Transcriptional regulators, LysR family

0.02

0.01

 

 CA_C3412

Predicted protein-S-isoprenylcysteine methyltransferase

0.22

0.06

 

 CA_C3422

Sugar:proton symporter (possible xylulose)

0.05

0.03

 

 CA_C3423

Acetyltransferase (ribosomal protein N-acetylase subfamily)

0.04

0.03

 

 CA_C3612

Hypothetical protein

0.18

0.00

BuOH

 CA_P0053

Xylanase, glycosyl hydrolase family 10

0.24

0.09

BuOH

 CA_P0054

Xylanase/chitin deacetylase family enzyme

0.24

0.07

BuOH

 CA_P0057

Putative glycoprotein or S-layer protein

0.21

0.13

BuOH

 CA_P0135

Oxidoreductase

0.25

0.21

 

 CA_P0136

AstB/chuR/nirj-related protein

0.25

0.23

 

 CA_P0174

Membrane protein

0.25

0.14

 
  1. aCymR indicates CymR regulon, BuOH indicates the genes to be down-regulated by butanol stress in an acidogenic chemostat in the study by Schwarz et al. [30]
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