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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]