Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

Rodionov, Dmitry A; Novichkov, Pavel S; Stavrovskaya, Elena D; Rodionova, Irina A; Li, Xiaoqing; Kazanov, Marat D; Ravcheev, Dmitry A; Gerasimova, Anna V; Kazakov, Alexey E; Kovaleva, Galina Yu; Permina, Elizabeth A; Laikova, Olga N; Overbeek, Ross; Romine, Margaret F; Fredrickson, James K; Arkin, Adam P; Dubchak, Inna; Osterman, Andrei L; Gelfand, Mikhail S

doi:10.1186/1471-2164-12-S1-S3

Table 1 Previously known TF regulons reconstructed in Shewanella spp.

From: Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

TF name	S.oneidensis MR-1	S. putrefaciens CN-32	S.putrefaciens W3-18-1	Shewanella sp. ANA-3	Shewanella sp. MR-4	Shewanella sp. MR-7	S. baltica OS155	S. denitrificans OS217	S. frigidimarina NCIMB 400	S.amazonensis SB2B	S. loihica PV-4	S. pealeana ATCC 700345	S.halifaxensis HAW-EB4	S. piezotolerans WP3	S. sediminis HAW-EB3	S.woodyi ATCCC 51908	Pseudomonas spp.	E.coli	Regulon functional role
AgaR	-	-	-	+	+	+	-	-	-	+	-	-	-	-	-	-	-	rs	GalNAc utilization
ArgR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Arginine biosynthesis
BetI	-	-	-	-	-	-	+	+	+	-	-	+	+	+	+	+	+	rs	Osmotic protection
BirA	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	Biotin biosynthesis
Crp	r	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	Global regulon
CueR	+	+	+	+	+	+	+	+	-	+	-	+	+	+	+	+	rs	rs	Copper efflux
Dnr	-	-	-	-	-	-	-	+	-	+	+	-	-	-	-	-	rs	-	Denitrification
FabR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	Fatty acid biosynthesis
FadR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Fatty acid degradation
Fnr	r	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	Global regulon
Fur	rs	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	rs	Iron homeostasis
GalR	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	rs	Galactose utilization
GcvA	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Glycine metabolism
GlmR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	r	-	LPS synthesis
GntR	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	rs	Gluconate utilization
HexR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	+	Central sugar metabolism
HutC	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	r	-	Histidine utilization
IlvY	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Isoleucine-valine synthesis
IscR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	Fe-S cluster assembly
LexA	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	rs	DNA damage stress
MetJ	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Methionine biosynthesis
MetR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	Methionine biosynthesis
ModE	+	-	-	+	+	+	+	-	-	-	-	-	-	-	-	-	+	rs	Molybdenium metabolism
NanR	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	rs	Sialic acid utilization
NarP	+	+	+	+	+	+	+	-	+	+	+	+	+	+	+	+	-	rs	Nitrate/nitrite respiration
NhaR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Osmotic stress protection
NikR	-	-	-	-	-	-	-	-	-	-	-	+	+	-	+	-	+	rs	Nickel uptake
NorR	-	+	+	+	+	+	-	-	+	+	+	+	+	+	+	+	+	rs	Nitrosative stress
NrdR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	Nucleotide metabolism
NrtR	rs	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	Nicotinamide utilization
NsrR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Nitrosative stress
NtrC	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	rs	Nitrogen assimilation
PdhR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Pyruvate metabolism
PsrA	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs	-	Fatty acid degradation
RbsR	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	+	rs	Ribose utilization
SdaR	+	+	+	+	+	+	+	-	+	-	+	+	+	+	+	+	+	r	Glycerate utilization
SoxR	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	+	+	rs	Superoxide stress
TorR	rs	-	-	+	+	+	+	-	+	+	+	+	+	+	+	+	-	rs	TMAO respiration
TrpR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Amino acid metabolism
TyrR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	rs*	rs	Amino acid metabolism
ZntR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	rs	Zinc efflux

The presence of orthologous transcription factors is shown by '+', 'r' and 'rs', whereas its absence is denoted by '-'. TFs with previously characterized target genes in model species are denoted by 'r'. TFs with previously known TFBSs at their target genes are denoted by 'rs'. Ortholog of TyrR in Pseudomonas spp. that was characterized as the phenylalanine and tyrosine catabolism regulator PhhR is marked by asterisk.

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ISSN: 1471-2164

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