FabR regulates Salmonella biofilm formation via its direct target FabB

BMC Genomics

Table 2 Putative FabR targets identified using ChIP-chip

Gene ID^a	Name^a	Possible FabR Target^b	Function^a	Functional Class^b
STM1100	hpaR (<)	IR hpaR-hpaG	4-Hydroxyphenylacetate catabolism	1
STM1101	hpaG (>)		4-Hydroxyphenylacetate catabolism	1
STM1336	rplT (>)	P pheS	50S ribosomal protein L20	2
STM1337	pheS (>)		Phenylalanyl-tRNA synthetase subunit alpha	3
STM2378	fabB (<)	IR fabB-STM2379	3-Oxoacyl-(acyl carrier protein) synthase I	4
STM2379	STM2379 (>)		5-Methylaminomethyl-2-thiouridine methyltransferase	5
STM2401	ddg (>)	DR ddg-yfdZ	Lipid A biosynthesis palmitoleoyl acyltransferase	6
STM2402	yfdZ (<)		Aminotransferase	7
STM2415	gltX (<)	IR gltX-valU	Glutamyl-tRNA synthetase	3
STM2416	valU (>)		tRNA	3
STM2615	STM2615 (<)	P STM2615	tRNA	3
STM2616	STM2616 (<)		Antirepressor-like protein	8
STM2616	STM2616 (<)	P STM2616	Antirepressor-like protein	8
STM2617	STM2617 (<)		Antiterminator-like protein	8
STM2989	metZ (>)	P metW	tRNA	3
STM2990	metW (>)		tRNA	3
STM3049	yqfA (<)	P yqfA	Putative hemolysin	6
STM3050	yqfB (<)		Hypothetical protein	5
STM3289	metY (<)	IR metY-argG	tRNA	3
STM3290.S	argG (>)		Argininosuccinate synthase	7
STM4148	nusG (>)	P rplK	Transcription antitermination protein	8
STM4149	rplK (>)		50S ribosomal protein L11	2
STM4150	rplA (>)	P rplJ	50S ribosomal protein L1	2
STM4151	rplJ (>)		50S ribosomal protein L10	2

^aSTM numbers, gene names, genomic orientation (< and > indicating minus and positive strand, respectively) and gene functions are taken from NCBI Refseq NC_003197 [86] and results are sorted according to their STM numbers
^bThe mentioned genes belong to the following functional classes: (1) Carbon compound degradation, (2) Ribosomal protein synthesis and modification, (3) Aminoacyl tRNA metabolism, (4) Fatty acid metabolism, (5) Conserved hypothetical protein, (6) Membrane homeostasis, (7) Amino acid biosynthesis, (8) RNA synthesis, RNA modification and DNA transcription
^bIR indicates that both genes are possible FabR targets since the FabR binding region was situated in the intergenic region between the two mentioned divergently transcribed genes and hence contains the (putative) promoters of both genes. P points at the (putative) promoter region of the mentioned gene since the intergenic region identified during the ChIP-chip analysis was situated between two genes transcribed in the same direction and hence only contains the (putative) promoter of this gene. DR indicates that probably none of the identified genes is a putative FabR target since both adjacent genes are convergently transcribed respective to the retained intergenic FabR binding region

ISSN: 1471-2164