Team:Imperial College London/M2/genes

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RcsB

Background:

RcsB is a transcription factor that forms part of a phosphorelay system. In response to membrane stress, RcsB is phosphorylated into its DNA binding form. In this state, it is able to regulate ~5% of the E.coli genome ⁴.

The Rcs Phosphorelay System:

In this system, RcsC encodes a membrane bound sensor kinase, while RcsB functions as the response regulator. The protein RcsA is an auxiliary activator protein that heterodimerises with RcsB to induce a mucoid phenotype. Levels of RcsA are controlled by the ATP dependent protease Lon.

RcsB upregulates the following genes:

Colanic Acid Biosynthesis:

wcaF

Putative colanic acid biosynthesis acetyltransferase ²

gmd

Codes for GDP-mannose 4,6-dehydratase which is a subunit of GDP-mannose 4,6-dehydratase. This enzyme is involved in colanic acid biosynthesis.

wcaD

Predicted colanic acid polymerase

wza

This codes for a lipoprotein that is required for colanic acid translocation through the outer membrane. The lipoprotein is a subunit of the capsular polysaccharide export apparatus.

fcl

Codes for a subunit of GDP-fucose synthase. This enzyme is involved in colanic acid biosynthesis.

General Protective:

ivy (Inhibitor of Vertebrate lysozyme)

Discovered in 2001 as the first bacterial lysozyme inhibitor. This Type-C lysozyme inhibitor resides in the periplasm.¹

MilC (Membrane-bound lysozyme inhibitor of Type C lysozyme)

This is a lipoprotein that resides in the membrane. ¹

OsmC (Osmotically-inducible protein C)

This protein provides defense against oxidative stress caused by exposure to organic hydroperoxides. ² ³

KatE

Codes for a subunit of heme d synthase / hydroperoxidase. This bacterial catalase protects against osmotic stress.

Global Regulators:

Sra (stationary-phase-induced ribosome-associated)

Sra is a sub-stoichiometric component of the 30S ribosomal subunit that is more abundant at stationary phase than during log phase growth.

rprA

rprA is a gene encoding a small RNA molecule that is involved in the post-transcriptional control of the alternative sigma factor, ("sigma S").

FtsA

FtsA is an essential cell division protein which colocalizes with FtsZ to the septal ring structure.

FtsZ

Essential cell division protein.

yfbR

dCMP phosphohydrolase

Membrane Proteins:

bdm (biofilm-dependent modulation protein)

OsmB

OsmB encodes an outer membrane lipoprotein.

OsmY

Hyperosmotically inducible periplasmic protein

PhnQ

ycfJ

Uncharacterized putative inner membrane protein.

ygaC

spy

ymgD

Putative periplasmic protein.

ypeC

Unknown function

ymgG

YbaY

Predicted outer membrane lipoprotein

References

1) [http://www.ncbi.nlm.nih.gov/pubmed/19136591 The Rcs two-component system regulates expression of lysozyme inhibitors and is induced by exposure to lysozyme]

2) [http://www.ncbi.nlm.nih.gov/pubmed/19346340 Gene Expression Induced in Escherichia coli O157:H7 upon Exposure to Model Apple Juice]

3) [http://www.ncbi.nlm.nih.gov/pubmed/14627744 Structural and functional features of the Escherichia coli hydroperoxide resistance protein OsmC.]

4) [http://www.ncbi.nlm.nih.gov/pubmed/16153174?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum The Rcs phosphorelay: a complex signal transduction system.]

	Gene ID	External ID	Name

	944840		mannose-6-phosphate isomerase

	945354		UDP-galactose-4-epimerase

	945357		galactose-1-phosphate uridylyltransferase

	945358		galactokinase

	945730		glucose-1-phosphate uridylyltransferase

	946560		predicted subunit with GalU

	946562		GDP-D-mannose dehydratase, NAD(P)-binding

	946563		bifunctional GDP-fucose synthetase: GDP-4-dehydro-6-deoxy-D-mannose epimerase/ GDP-4-dehydro-6-L-deoxygalactose reductase

	946571		UDP-glucose 6-dehydrogenase

	946574		phosphomannomutase

	Structure	Substance ID	Compound ID	External ID	Name

		2192	271	CA+2	calcium ion; Calcium cation; calcane; Calcium ions

		2992	15938971	NAD	coenzyme I; NAD-oxidized; nchembio867-comp14; DPN-ox

		2994	4349538	NADH	NAD-reduced; DPNH; NADH; NADH2

		2719	21604863	FRUCTOSE-6P	fruc6p; fructose-6P; fructose-6-P; D-fructose-6-P

		2115	7058055	ADP	2hmv; 2fr8; 2ja3; ZINC03861152

		2777	7058167	GTP	guanosine-triphosphate; guanosine 5"-triphosphate; guanylyl imidodiphosphate; nchembio.2007.33-comp6

		3279	7058168	UTP	uridine-triphosphate; uridine 5"-triphosphate; uridine-5"-triphosphate; uridine 5"-triphosphate(4-)

		3092	4097574	PPI	diphosphate; pyrophosphate; diphosphate(3-); hydrogen diphosphate

		2952	888	MG+2	magnesium ion; Magnesium cation; Magnesane; MAGNESIUM

		57393555	1567	2-MERCAPTOETHANOL	2-mercaptoethanol; Mercaptoethanol; Thioglycol; Monothioglycol

	Gi	Accession	Name	pig

Identical Protein

16129197

NP_415752

glucose-1-phosphate uridylyltransferase [Escherichia coli str. K-12 substr. MG1655]

3 Identical Proteins

2506454

P09148

RecName: Full=Galactose-1-phosphate uridylyltransferase; Short=Gal-1-P uridylyltransferase; AltName: Full=UDP-glucose--hexose-1-phosphate uridylyltransferase

16128726

NP_415279

galactose-1-phosphate uridylyltransferase [Escherichia coli str. K-12 substr. MG1655]

89107609

AP_001389

galactose-1-phosphate uridylyltransferase [Escherichia coli str. K-12 substr. W3110]

Identical Protein

16129993

NP_416557

GDP-D-mannose dehydratase, NAD(P)-binding [Escherichia coli str. K-12 substr. MG1655]

3 Identical Proteins

117279

P24175

RecName: Full=Phosphomannomutase; Short=PMM

16129988

NP_416552

phosphomannomutase [Escherichia coli str. K-12 substr. MG1655]

89108868

AP_002648

phosphomannomutase [Escherichia coli str. K-12 substr. W3110]

3 Identical Proteins

120920

P09147

RecName: Full=UDP-glucose 4-epimerase; AltName: Full=UDP-galactose 4-epimerase; AltName: Full=Galactowaldenase

49176045

NP_415280

UDP-galactose-4-epimerase [Escherichia coli str. K-12 substr. MG1655]

89107610

AP_001390

UDP-galactose-4-epimerase [Escherichia coli str. K-12 substr. W3110]

3 Identical Proteins

126724

P00946

RecName: Full=Mannose-6-phosphate isomerase; AltName: Full=Phosphomannose isomerase; Short=PMI; AltName: Full=Phosphohexomutase

49176125

NP_416130

mannose-6-phosphate isomerase [Escherichia coli str. K-12 substr. MG1655]

89108454

AP_002234

mannose-6-phosphate isomerase [Escherichia coli str. K-12 substr. W3110]

3 Identical Proteins

2499085

P76373

RecName: Full=UDP-glucose 6-dehydrogenase; Short=UDP-Glc dehydrogenase; Short=UDP-GlcDH; Short=UDPGDH

16129969

NP_416532

UDP-glucose 6-dehydrogenase [Escherichia coli str. K-12 substr. MG1655]

89108849

AP_002629

UDP-glucose 6-dehydrogenase [Escherichia coli str. K-12 substr. W3110]

Identical Protein

16129982

NP_416546

predicted subunit with GalU [Escherichia coli str. K-12 substr. MG1655]

Identical Protein

16128725

NP_415278

galactokinase [Escherichia coli str. K-12 substr. MG1655]

3 Identical Proteins

2506453

P32055

RecName: Full=GDP-L-fucose synthetase; AltName: Full=GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase

16129992

NP_416556

bifunctional GDP-fucose synthetase: GDP-4-dehydro-6-deoxy-D-mannose epimerase/ GDP-4-dehydro-6-L-deoxygalactose reductase [Escherichia coli str. K-12 substr. MG1655]

89108872

AP_002652

bifunctional GDP-fucose synthetase: GDP-4-dehydro-6-deoxy-D-mannose epimerase and GDP-4-dehydro-6-L-deoxygalactose reductase [Escherichia coli str. K-12 substr. W3110]

3 Identical Proteins

16129989

NP_416553

mannose-1-phosphate guanyltransferase [Escherichia coli str. K-12 substr. MG1655]

33112662

P24174

RecName: Full=Mannose-1-phosphate guanylyltransferase; AltName: Full=GDP-mannose pyrophosphorylase; Short=GMPP; Short=GMP

89108869

AP_002649

mannose-1-phosphate guanyltransferase [Escherichia coli str. K-12 substr. W3110]