Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

Maksim Shestov; Santiago Ontañón; Aydin Tozeren

doi:10.1186/s12864-015-1957-7

BMC Genomics

Table 4 Nonpathogen-linked gene circuits in bacterial strains. The columns identify pathways, circuits, nonpathogen-linked orthologs within the circuit; and genera expressing the circuit

From: Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

	Pathway	Circuit	Orthologs	Genera
1	Steroid biosynthesis	Squalene to 24,25-Dihydro-lanosterol	SQLE, ERG1, E5.4.99.7, LSS, ERG7, DHCR24	C. coralloides, F. taffensis, M. capsulatus, M. alcaliphilum, S. aurantiaca
7	Arginine and proline metabolism	N-Acetyl-glutamate - N-Acetyl-ornithine	argB, ARG56, argC, lysY, ARG56, E2.6.1.11, argD, argD, lysJ	E. coli, S. enterica, S. aureus, L. monocytogenes, M. tuberculosis
3	Biosynthesis of 12-, 14- and 16-membered macrolides	Propanoyl-CoA to Erythromycin A	E2.3.1.94, eryF, eryBV, eryCIII, eryCII, eryG, eryK	F. alni, S. erythraea,
2	Lysine biosynthesis	L-2-Amino adipate to Pyrrolysine	lysX, lysZ, lysY, lysJ, E2.4.1.173, pylB, pylC, pylD	T. thermophilus*, P. mucilaginosus, C. sp., D. hafniense, M. ruber
5	Glycine, serine and threonine metabolism	Choline - Glycine	codA, gbsB, BHMT, DMGDH, SARDH	B. amyloliquefaciens, B. subtilis, S. meliloti, R. sphaeroides, B. licheniformis
6	Arginine and proline metabolism	Creatine Pathway	GAMT, E2.7.3.2, E3.5.3.3, E3.5.1.59, hyuA, hyuB, E3.5.4.21	H. pylori*, P. putida, C. sp., A. mediterranei, G. sp.
11	Type I polyketide structures	Rifamycin B	rifA, rif14, rifB, rif20, rifC_D, rifE, rifF, asm9, rif19	A. mediterranei*, F. sp., A. mirum, M. aurantiaca, M. sp.
4	Biosynthesis of 12-, 14- and 16-membered macrolides	2-Methylbutanoyl to Avermectin	aveA, aveE, aveF, aveD, aveBI	S. avermitilis.
8	Streptomycin biosynthesis	scyllo-inosamine	stsE, strB1, E2.4.2.27, strK, K12570, aphD, strA	S. griseus
9	Type I polyketide structures	Erythromycin A	eryK, E2.3.1.94, eryF, E2.3.1.94, eryCIII, eryCII, E2.3.1.94, eryBV	F. alni, S. erythraea.
10	Type I polyketide structures	Avermectin A1a	aveA, aveBI, aveE, aveF, aveD	S. avermitilis,
12	Type I polyketide structures	Myalamid S	mxaB, mxaE_D, mxaF	G. violaceus, H. ochraceum, H. aurantiacus, M. xanthus, N. punctiforme
13	Biosynthesis of type II polyketide backbone	7,9,12-Octaketides	actI1, actI2, actI3, actIII, actVII	A. mediterranei, F. sp., A. missouriensis, C. acidiphila, C. epipsammum
14	Biosynthesis of type II polyketide products	7,9,12-Octaketides - Actinorhodin	actVI1, RED1, actVI3, actVI2, actIV, actVI4, actVA6, actVIA, actVA5, actVB	A. mediterranei*, F. sp., M. abscessus, S. cattleya, A. ferrooxidans
15	Serotonergic synapse	Signal transduction	PLA2G4, CPLA2, ALOX5, PTGS2, COX2, PTGS2, COX2	R. sphaeroides*, C. coralloides, G. obscurus, M. nodulans, M. sp.
16	Insulin signaling pathway	Glycogenesis/ antilipolysos	GYS, CALM, PHKA_B, PRKAR	S. sp., C. sp., A. sp., B. coagulans, C. sp.
17	Chemical carcinogenesis	Azo dyes/Liver cancer/Bladder cancer	PTGS2, COX2, CYP1A1	R. sphaeroides*, G. obscurus, M. mediterranea, M. nodulans, M. sp.

The symbol * indicates those genera for which the circuitry was linked to synergy via within genus comparison

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