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

Santos, Juliana S.; da Silva, Carolina A. P. T.; Balhesteros, Heloise; Lourenço, Rogério F.; Marques, Marilis V.

doi:10.1186/s12864-015-1845-1

BMC Genomics

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 limitation^c
Carbohydrate Metabolism
CC_1764	CCNA_01841	isocitrate lyase	0.11	71.6^d	Yes
CC_1765	CCNA_01843	malate synthase	0.10	88.7^d	Yes
CC_3655	CCNA_03770	malate dehydrogenase	0.06	2.1	No
CC_3580	CCNA_03695	aldehyde dehydrogenase	0.25	82.4^d	Yes
CC_3581	CCNA_03696	acetyl-CoA synthetase	0.25	20.0^d	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	8.1^d	No
Motility
CC_0793	CCNA_00835	flagellin FljN	0.17	0.7	No
CC_1460	CCNA_01527	flagellin FljL	0.33	0.2^d	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	10.1^d	Yes
CC_2880	CCNA_02974	toxin protein relE₃	0.39	14.1^d	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	4.5^d	Yes
CC_1343	CCNA_01405	GIY-YIG domain protein	0.32	16.9^d	Yes
CC_2696	CCNA_02779	LysM family peptidoglycan binding protein	0.35	6.6^d	No
CC_2869	CCNA_02962	HicB-family RNase H fold protein	0.30	11.9^d	Yes
CC_3153	CCNA_03255	PemK-family protein	0.34	4.5^d	Yes
CC_3582	CCNA_03697	ligand-binding SRPBCC domain protein	0.25	14.5^d	No
Hypothetical
CC_0559	CCNA_00594	Hypothetical protein	0.14	10.6^d	Yes
CC_0681	Unannotated		0.05	4.4^d	No
CC_0682	Unannotated		0.19	6.4^d	No
CC_0781	CCNA_00822	Hypothetical protein	0.10	13.2^d	Yes
CC_0997	Unannotated		0.31	22.5^d	No
CC_1392	CCNA_01458	Hypothetical protein	0.34	9.3^d	No
CC_2184	Unannotated		0.18	12.4^d	Yes
CC_2348	CCNA_02433	Hypothetical protein	0.26	6.6^d	Yes
CC_2645	CCNA_02728	Hypothetical protein	0.26	38.1^d	Yes
CC_3207	CCNA_03313	Hypothetical protein	0.33	38.7^d	Yes
CC_3654	CCNA_03769	Hypothetical protein	0.23	5.8^d	No

^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
^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
^cGenes upregulated in carbon limitation in previous work [26]
^dGenes significantly up- or downregulated at stationary phase with respect to exponential phase

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ISSN: 1471-2164

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