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 2 Novel TF regulons predicted and 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	Regulon functional role
A. Regulons inferred from the analysis of metabolic pathways
AlgR*	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	Hexuronate utilization
AraR*	-	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	Arabinose utilization
BglR*	-	-	-	-	-	-	+	+	+	+	-	-	-	+	-	+	Beta-glucoside utilization
HmgR*	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Tyrosine degradation
HypR*	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Hydroxyproline utilization
LiuR	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Amino acid utilization
LldR*	+	+	+	+	+	+	+	-	+	+	+	+	+	+	+	-	Lactate utilization
MalR*	+	-	-	+	+	+	+	+	+	+	+	-	-	+	-	+	Maltodextrin utilization
ManR1*	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	Mannose utilization
ManR2*	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	Mannose utilization
MtlR2	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	Mannitol utilization
NagR	+	+	+	+	+	+	+	+	-	+	+	+	+	+	+	+	GlcNAc utilization
PflR*	-	+	+	-	-	-	-	-	+	+	+	+	+	+	+	+	Formate metabolism
PrpR*	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Propionate utilization
PUR*	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Purine biosynthesis
ScrR*	-	-	-	+	+	+	+	-	+	-	-	-	-	-	-	-	Sucrose utilization
TreR*	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	Trehalose utilization
XltR*	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	Xylitol utilization
B. Regulons inferred from the analysis of chromosomal gene clusters
AzrR*	+	+	+	+	+	+	+	-	-	+	+	+	+	+	+	+	Superoxide stress
CalR*	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	Aromatics utilization
CueR2	-	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	Copper efflux
DeoR*	+	+	+	+	-	-	-	-	-	-	-	+	+	+	+	+	Nucleoside utilization
PnuR*	+	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	NAD metabolism
SO0072	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	ABC efflux transporter
SO0082	+	-	-	-	+	-	+	-	+	-	-	-	-	-	-	-	Benzoate degradation
SO0193	+	+	+	+	+	+	+	-	+	+	+	-	-	-	-	-	Phospholipid synthesis
SO0734	+	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	hypothetical transporter
SO1393	+	-	-	+	+	+	-	-	-	-	+	-	-	-	-	-	hypothetical
SO1415	+	-	-	-	+	-	-	-	-	-	+	+	+	-	+	-	flavocytochrome c
SO1578	+	-	-	+	+	+	+	-	-	+	+	-	-	-	-	+	Glutathione detoxification
SO1703	+	+	+	+	+	+	+	+	-	+	+	+	+	+	+	-	multidrug efflux
SO1758	+	+	+	+	+	+	+	-	-	+	+	-	-	-	+	+	hypothetical
SO2282	+	+	+	+	+	+	+	-	-	+	-	+	+	+	-	+	Amino acid efflux
SO3277	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	multidrug efflux
SO3385	+	+	+	+	+	+	+	-	-	-	-	-	-	-	-	-	hypothetical
SO3393	+	+	+	+	+	+	+	+	+	+	+	-	-	+	+	+	xenobiotic reductase
SO3494	+	+	+	+	+	+	+	+	+	-	-	-	-	-	-	-	multidrug efflux
SO3627	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	flavocytochrome c
SO4326	+	-	-	+	-	-	-	-	-	+	-	+	+	+	+	+	multidrug efflux
SO4468	+	+	+	+	+	+	+	+	-	+	-	-	-	+	+	-	hypothetical
SO4705	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	hypothetical

The new TF names introduced in this work are marked by asterisks.

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ISSN: 1471-2164

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