Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain.
Salmonella are closely related to commensal Escherichia coli but have gained virulence factors enabling them to behave as enteric pathogens. Less well studied are the similarities and differences that exist between the metabolic properties of these organisms that may contribute toward niche adaptation of Salmonella pathogens. To address this, we have constructed a genome scale Salmonella metabolic model (iMA945). The model comprises 945 open reading frames or genes, 1964 reactions, and 1036 metabolites. There was significant overlap with genes present in E. coli MG1655 model iAF1260. In silico growth predictions were simulated using the model on different carbon, nitrogen, phosphorous, and sulfur sources. These were compared with substrate utilization data gathered from high throughput phenotyping microarrays revealing good agreement. Of the compounds tested, the majority were utilizable by both Salmonella and E. coli. Nevertheless a number of differences were identified both between Salmonella and E. coli and also within the Salmonella strains included. These differences provide valuable insight into differences between a commensal and a closely related pathogen and within different pathogenic strains opening new avenues for future explorations.
AbuOun
Manal
M
Department of Food and Environmental Safety, Veterinary Laboratories Agency (Weybridge), Addlestone, Surrey KT153NB, United Kingdom. m.abuoun@vla.defra.gsi.gov.uk
Suthers
Patrick F
PF
Jones
Gareth I
GI
Carter
Ben R
BR
Saunders
Mark P
MP
Maranas
Costas D
CD
Woodward
Martin J
MJ
Anjum
Muna F
MF
D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial / Q000502:physiology; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000502:physiology; D012477:Salmonella enteritidis / Q000235:genetics* / Q000378:metabolism*; D012486:Salmonella typhimurium / Q000235:genetics* / Q000378:metabolism*; D013045:Species Specificity
Nature. 2001 Oct 25;413(6858):852-6
11677609
Science. 1996 Jan 26;271(5248):470-7
8560259
Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17480-4
17088549
Nat Biotechnol. 2008 Jun;26(6):659-67
18536691
BMC Syst Biol. 2009 Apr 08;3:38
19356237
J Bacteriol. 2001 Apr;183(8):2463-75
11274105
Vet Rec. 1992 Oct 24;131(17):386-8
1455584
Biochemistry. 1990 Feb 20;29(7):1749-56
2184888
J Bacteriol. 1976 Aug;127(2):706-18
783117
PLoS Comput Biol. 2008 Oct;4(10):e1000210
18974823
Nucleic Acids Res. 2000 Dec 15;28(24):4974-86
11121489
BMC Bioinformatics. 2003 Sep 11;4:41
12969510
J Bacteriol. 2004 Mar;186(6):1629-37
14996793
J Bacteriol. 1996 Jan;178(1):111-20
8550403
Microbiol Mol Biol Rev. 2001 Dec;65(4):523-69, table of contents
11729263
Science. 1997 Sep 5;277(5331):1453-62
9278503
Epidemiol Infect. 1990 Aug;105(1):21-7
2200698
J Bacteriol. 2001 Oct;183(19):5725-32
11544236
Nat Rev Genet. 2006 Feb;7(2):130-41
16418748
Mol Syst Biol. 2006;2:2006.0008
16738554
J Gen Microbiol. 1987 Feb;133(2):347-51
3309152
J Biol Chem. 1969 Oct 10;244(19):5382-91
4899017
Mol Syst Biol. 2007;3:121
17593909
Proc Natl Acad Sci U S A. 1973 Jun;70(6):1841-5
4124306
J Bacteriol. 1997 Dec;179(24):7631-7
9401019
Infect Immun. 2005 Dec;73(12):7894-905
16299280
J Bacteriol. 2004 Sep;186(17):5883-98
15317794
J Bacteriol. 1994 Sep;176(17):5474-82
8071226
Genetics. 1978 Dec;90(4):673-81
105963
Arch Microbiol. 2007 May;187(5):415-24
17180672
J Bacteriol. 1985 Nov;164(2):731-40
3902796
FEMS Microbiol Rev. 2009 Jan;33(1):191-205
19054113
Mol Microbiol. 2005 Mar;55(6):1911-24
15752209
J Bacteriol. 2003 Oct;185(20):6042-50
14526015
BMC Bioinformatics. 2007 Jun 20;8:212
17584497
J Bacteriol. 1983 Dec;156(3):1019-24
6358185
Arch Microbiol. 2001 Jul;176(1-2):1-8
11479697
Gene. 1995 Dec 1;166(1):11-7
8529872
Infect Immun. 1998 Sep;66(9):4305-12
9712782
J Bacteriol. 2006 Dec;188(23):8259-71
17012394
Biotechnol Bioeng. 2000 Mar 20;67(6):872-85
10699864
J Biol Chem. 1971 May 25;246(10):3320-9
4930059
Mol Gen Genet. 1983;189(2):337-9
6343795
J Bacteriol. 1981 Sep;147(3):805-19
6115851
Nature. 2001 Oct 25;413(6858):848-52
11677608
J Gen Microbiol. 1983 Jan;129(1):75-84
6339679
J Bacteriol. 2003 Jan;185(2):553-63
12511502
J Bacteriol. 1973 Jul;115(1):307-15
4717519
Annu Rev Med. 2001;52:259-74
11160778
Nucleic Acids Res. 2008 Jan;36(Database issue):D623-31
17965431
Mol Gen Genet. 1994 Jun 15;243(6):674-80
8028584
Euro Surveill. 1997 Nov;2(11):81-84
12631789
J Bacteriol. 1999 Nov;181(22):7126-30
10559180
J Bacteriol. 1980 Jul;143(1):302-6
6995433
PLoS Comput Biol. 2009 Mar;5(3):e1000308
19282964
J Bacteriol. 2003 Aug;185(16):4956-72
12897016
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
18077471
J Bacteriol. 1998 Jul;180(14):3517-21
9657991
Genome Biol. 2003;4(9):R54
12952533
Genome Res. 2001 Jul;11(7):1246-55
11435407
J Biol Chem. 1999 Oct 8;274(41):29358-65
10506196
J Bacteriol. 1996 May;178(10):2941-7
8631685
J Bacteriol. 1999 Jan;181(1):47-54
9864311
J Bacteriol. 1996 Sep;178(18):5438-46
8808933
FEMS Microbiol Lett. 1992 Sep 15;75(2-3):149-54
1398030
J Bacteriol. 1998 Mar;180(5):1166-73
9495755
J Biol Chem. 1997 Sep 12;272(37):23031-6
9287300
PLoS Comput Biol. 2009 Feb;5(2):e1000285
19214212
Nat Rev Microbiol. 2006 Jan;4(1):46-56
16357860
Mol Microbiol. 1993 Jul;9(1):165-72
8412661
Nature. 2004 May 6;429(6987):92-6
15129285
Nature. 2000 May 18;405(6784):299-304
10830951