Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli

Kumka, Joseph E.; Bauer, Carl E.

doi:10.1186/s12864-015-2162-4

Table 1 FnrL directly regulated genes based on ChIP-seq signal with corresponding RNA-seq expression change that also contain a consensus binding sequence

From: Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli

Locus ID	Gene Name	Description	Recognition Sequence	Enrichment	Regulation	Fold Change
COG C: Energy production and conversion
RCC01157	ccoN	cbb ₃-type cytochrome c oxidase subunit I	TTGATCAAGGTCAA^b	25	+	1.55
RCC01157	ccoN	cbb ₃-type cytochrome c oxidase subunit I	ATGATGTCGATCAA^a	25	+	1.55
RCC00728	NnrU family protein	NnrU family protein	CTGCCGCAGATCAA^a	4	+	1.47
RCC00732	sdhD	succinate dehydrogenase	ATGATGAGCGTCAA^b	3	+	1.41
RCC00022	Oxidoreductase	oxidoreductase	ATGATTTACCGCAA^a	5	+	1.38
COG E: Amino acid transport and metabolism
RCC01724	speB1	agmatinase	TTGATCTGCGTCAA^b	10	+	1.33
COG F: Nucleotide transport and metabolism
RCC00400	pyrB	aspartate carbamoyltransferase	CTGACGCAGATCAA^a	10	+	1.47
COG G: Carbohydrate transport and metabolism
RCC00731	sdhC	succinate dehydrogenase, cytochrome b556 subunit	ATGATGAGCGTCAA^a	3	+	1.53
COG I: Lipid transport and metabolism
RCC00480	rpsU	30S ribosomal protein S21	CTGATGCAACTCAA^b	4	+	1.57
COG J: Translation, ribisomal tructure and biogenesis
RCC01495	fusA	translation elongation factor G	TTGGCATGGGTCAA^b	17	+	3.48
COG L: Replication, recombination and repair
RCC03240	ATPase AAA	K01144 exodeoxyribonuclease V	ATGCGCCAGATCAA^a	4	-	-1.34
RCC02193	DNA-3-methyladenine glycosylase II	K01247 DNA-3-methyladenine glycosylase II	ATGACGCGGATCAA^a	4	-	–1.97
COG M: Cell wall/membrane/envelope biogenesis
RCC02479	lipoprotein	lipoprotein	CTGATGCAGCGCAA^b	13	+	1.42
COG N: Cell motility
RCC00481	mcpI	methyl-accepting chemotaxis protein McpI	CTGACCGAGATCAA^a	4	-	–1.53
RCC03524	flagellar FlaF family protein	K06602 flagellar protein FlaF	CTGATCGACATCAA^a	4	-	–1.87
RCC03523	flbT	flagellin synthesis repressor protein FlbT	CTGATCGACATCAA^b	4	-	–2.14
COG O: Post-translational modification, protein turnover, and chaperones
RCC01156	UspA domain-containing protein	UspA domain-containing protein	TTGACGCGGATCAA^b	26	+	5.21
RCC01723	ccpA	cytochrome-c peroxidase	TTGATCTGCGTCAA^b	10	+	3.81
RCC02829	hypothetical protein	K03699 putative hemolysin	TTGACCCTCGTCAA^a	6	-	–1.64
COG R: General function prediction only
RCC02684	polyphosphate kinase 2	polyphosphate kinase 2	TTGATGCGTGTCAA^b	14	+	2.25
RCC02665	hemolysin-type calcium-binding	hemolysin-type calcium-binding	ATGACCGGCGTCAA^a	9	+	1.46
COG S: Function unknown
RCC00435	hypothetical protein	hypothetical protein	CTGACCCAGATCAA^b	21	+	9.19
RCC00901	hypothetical protein	hypothetical protein	TTGACACGGGTCAA^b	10	+	6.87
RCC00747	hypothetical protein	hypothetical protein	ATGACGCAGATCAA^b	5	+	3.78
RCC00424	hypothetical protein	hypothetical protein	ATGATTCAGATCAA^b	20	+	3.51
RCC02321	hypothetical protein	hypothetical protein	ATGATCCGGATCAA^b	26	+	2.17
RCC02988	hypothetical protein	hypothetical protein	TTGACCCAGATCAA^b	8	-	–1.41
RCC01027	hypothetical protein	hypothetical protein	TTGACCAAGGTCAA^b	6	-	–1.64
COG T: Signal transduction mechanisms
RCC02849	dorS	DMSO/TMAO-sensor hybrid histidine kinase	TTGATCGGGATCAA^a	26	+	4.53
RCC02590	dksA	DnaK suppressor protein	TTGATTCAGGTCAA^b	28	+	1.79
COG X: Photosynthesis
RCC00667	aerR	regulatory CrtJ antirepressor AerR	ATGCTCGAGTTCAA^b	8	+	1.39
RCC00666	bchF	2-vinyl bacteriochlorophyllide hydratase	ATGACATGGGTCAA^b	8	+	1.39

Recognition sequences were determined using MEME server
^aSequence is found within the coding region of the gene
^bSequence is found in the upstream intergenic or promoter region

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ISSN: 1471-2164

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