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Table 3 Genes downregulated in the cspC mutant at stationary phase

From: CspC regulates the expression of the glyoxylate cycle genes at stationary phase in Caulobacter

Gene CB15 Gene NA1000 Predicted function Fold change (∆cspC/WT)a Fold change (WTstat/WTexp)b Upregulated in carbon limitationc
Carbohydrate Metabolism     
CC_1764 CCNA_01841 isocitrate lyase 0.11 71.6d Yes
CC_1765 CCNA_01843 malate synthase 0.10 88.7d Yes
CC_3655 CCNA_03770 malate dehydrogenase 0.06 2.1 No
CC_3580 CCNA_03695 aldehyde dehydrogenase 0.25 82.4d Yes
CC_3581 CCNA_03696 acetyl-CoA synthetase 0.25 20.0d No
Amino acid Metabolism     
CC_0167 CCNA_00166 putative transglutaminase-like cysteine proteinase 0.20 2.2 Yes
CC_2533 CCNA_02616 4-hydroxyphenylpyruvate dioxygenase 0.36 1.2 No
Transport      
CC_0579 CCNA_00615 TonB-dependent receptor 0.22 8.1d No
Motility      
CC_0793 CCNA_00835 flagellin FljN 0.17 0.7 No
CC_1460 CCNA_01527 flagellin FljL 0.33 0.2d No
CC_1461 CCNA_01528 flagellin FljK 0.28 0.9 Yes
CC_2948 CCNA_03043 type IV pilin protein PilA 0.25 0.8 No
CC_3025 CCNA_03120 chemotaxis protein CheW 0.14 1.4 Yes
Oxidative stress response     
CC_1777 CCNA_01855 iron/manganese superoxide dismutase 0.35 1.3 No
Toxin-antitoxin systems     
CC_2513 CCNA_02598 toxin protein relE2 0.39 10.1d Yes
CC_2880 CCNA_02974 toxin protein relE3 0.39 14.1d No
Signal Transduction and Transcription    
CC_0903 CCNA_00948 CtrA inhibitory protein SciP 0.31 1.0 Yes
Proteins with no assigned category    
CC_0451 CCNA_00483 Zn-dependent hydrolase, glyoxalase II family 0.33 0.5 No
CC_0557 CCNA_00592 ferritin superfamily protein 0.34 2.7 Yes
CC_0679 CCNA_00718 abortive infection protein 0.30 2.1 Yes
CC_0707 CCNA_00744 GIY-YIG endonuclease domain protein 0.28 4.5d Yes
CC_1343 CCNA_01405 GIY-YIG domain protein 0.32 16.9d Yes
CC_2696 CCNA_02779 LysM family peptidoglycan binding protein 0.35 6.6d No
CC_2869 CCNA_02962 HicB-family RNase H fold protein 0.30 11.9d Yes
CC_3153 CCNA_03255 PemK-family protein 0.34 4.5d Yes
CC_3582 CCNA_03697 ligand-binding SRPBCC domain protein 0.25 14.5d No
Hypothetical     
CC_0559 CCNA_00594 Hypothetical protein 0.14 10.6d Yes
CC_0681 Unannotated   0.05 4.4d No
CC_0682 Unannotated   0.19 6.4d No
CC_0781 CCNA_00822 Hypothetical protein 0.10 13.2d Yes
CC_0997 Unannotated   0.31 22.5d No
CC_1392 CCNA_01458 Hypothetical protein 0.34 9.3d No
CC_2184 Unannotated   0.18 12.4d Yes
CC_2348 CCNA_02433 Hypothetical protein 0.26 6.6d Yes
CC_2645 CCNA_02728 Hypothetical protein 0.26 38.1d Yes
CC_3207 CCNA_03313 Hypothetical protein 0.33 38.7d Yes
CC_3654 CCNA_03769 Hypothetical protein 0.23 5.8d No
  1. aValues are fold changes in the expression levels comparing the null cspC mutant (∆cspC) with wild type cells (WT). The values are the means of three biological replicates
  2. bValues are fold changes in the expression levels comparing wild type cells at stationary phase (WT stat) versus exponential phase (WT exp). The values are the means of two biological replicates
  3. cGenes upregulated in carbon limitation in previous work [26]
  4. dGenes significantly up- or downregulated at stationary phase with respect to exponential phase