Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043.
BACKGROUND
Chromohalobacter salexigens (formerly Halomonas elongata DSM 3043) is a halophilic extremophile with a very broad salinity range and is used as a model organism to elucidate prokaryotic osmoadaptation due to its strong euryhaline phenotype.


RESULTS
C. salexigens DSM 3043's metabolism was reconstructed based on genomic, biochemical and physiological information via a non-automated but iterative process. This manually-curated reconstruction accounts for 584 genes, 1386 reactions, and 1411 metabolites. By using flux balance analysis, the model was extensively validated against literature data on the C. salexigens phenotypic features, the transport and use of different substrates for growth as well as against experimental observations on the uptake and accumulation of industrially important organic osmolytes, ectoine, betaine, and its precursor choline, which play important roles in the adaptive response to osmotic stress.


CONCLUSIONS
This work presents the first comprehensive genome-scale metabolic model of a halophilic bacterium. Being a useful guide for identification and filling of knowledge gaps, the reconstructed metabolic network iOA584 will accelerate the research on halophilic bacteria towards application of systems biology approaches and design of metabolic engineering strategies.
Department of Bioengineering, Marmara University, 34722, Istanbul, Turkey.
Ozlem
O
Ates
Ebru Toksoy
ET
Oner
Kazim Y
KY
Arga
D000222:Adaptation, Physiological; D000599:Amino Acids, Diamino / Q000096:biosynthesis; D001622:Betaine / Q000378:metabolism; D002794:Choline / Q000096:biosynthesis; D055353:Chromohalobacter / Q000235:genetics* / Q000378:metabolism* / Q000502:physiology; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008954:Models, Biological; D010641:Phenotype
D000599:Amino Acids, Diamino; D001622:Betaine; C045628:ectoine; D002794:Choline
Nat Rev Microbiol. 2009 Feb;7(2):129-43
19116616
Nat Protoc. 2010 Jan;5(1):93-121
20057383
Methods Mol Biol. 2004;267:183-208
15269425
Biotechnol Bioeng. 2010 Sep 1;107(1):124-33
20506292
Genome Inform. 2006;17(2):46-56
17503378
Extremophiles. 2005 Aug;9(4):275-9
15902510
PLoS Comput Biol. 2008 Oct;4(10):e1000210
18974823
Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1777-82
17267599
Appl Microbiol Biotechnol. 2008 Oct;80(5):849-62
18758767
Microbiology (Reading). 2004 Sep;150(Pt 9):3051-3063
15347763
BMC Syst Biol. 2010 Aug 16;4:114
20712863
Appl Environ Microbiol. 1998 Oct;64(10):4095-7
9758852
Appl Environ Microbiol. 2007 May;73(10):3343-7
17369334
Nat Biotechnol. 2008 Oct;26(10):1155-60
18846089
Proc Natl Acad Sci U S A. 2000 May 9;97(10):5528-33
10805808
Biotechnol Bioeng. 2007 Aug 1;97(5):1246-58
17252576
Nucleic Acids Res. 2009 Jan;37(Database issue):D588-92
18984617
Nat Rev Genet. 2006 Feb;7(2):130-41
16418748
Mol Syst Biol. 2007;3:121
17593909
J Bacteriol. 2009 Jun;191(12):4015-24
19376871
BMC Syst Biol. 2008 Sep 16;2:79
18793442
BMC Syst Biol. 2008 Aug 07;2:71
18687109
Nucleic Acids Res. 2010 Jan;38(Database issue):D361-5
19906735
Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
19880382
BMC Microbiol. 2005 Mar 07;5:8
15752426
Mol Syst Biol. 2006;2:2006.0004
16738551
World J Microbiol Biotechnol. 1995 Jan;11(1):85-94
24414413
Nucleic Acids Res. 2003 Jul 1;31(13):3784-8
12824418
BMC Bioinformatics. 2006 Mar 06;7:111
16519800
Adv Microb Physiol. 1995;37:272-328
8540423
BMC Microbiol. 2005 Jun 27;5:39
15982422
J Bacteriol. 2002 Aug;184(16):4582-93
12142428
Mol Biosyst. 2008 Feb;4(2):148-59
18213408
J Bacteriol. 1976 Sep;127(3):1550-7
8432
Nucleic Acids Res. 2005 Oct 24;33(19):6083-9
16246909
Genome Res. 2003 Feb;13(2):244-53
12566402
Biotechnol Bioeng. 2009 Feb 1;102(2):583-97
18985611
Bioinformatics. 2002;18 Suppl 1:S225-32
12169551
Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12176-81
11016950
Genome Res. 2004 Jul;14(7):1298-309
15197165
J Biol Chem. 2007 Sep 28;282(39):28791-28799
17573341
Brief Bioinform. 2009 Jul;10(4):435-49
19287049
Int J Syst Evol Microbiol. 2001 Jul;51(Pt 4):1457-1462
11491346
J Bacteriol. 2008 Apr;190(8):2790-803
18192387
J Bacteriol. 2005 Aug;187(16):5818-30
16077130
BMC Syst Biol. 2009 Jan 28;3:15
19175927
Trends Microbiol. 2005 Nov;13(11):550-8
16169729
BMC Bioinformatics. 2006 Jun 13;7:296
16772023
Appl Environ Microbiol. 2010 Jun;76(11):3575-89
20363778
J Bacteriol. 1996 Dec;178(24):7221-6
8955405
Methods Mol Biol. 2003;226:3-6
12958470
J Ind Microbiol Biotechnol. 2002 Jan;28(1):56-63
11938472
Nature. 1997 Nov 27;390(6658):364-70
9389475
Genome Biol. 2003;4(9):R54
12952533
Int Microbiol. 2008 Sep;11(3):151-61
18843593
Metab Eng. 2003 Oct;5(4):264-76
14642354
Curr Opin Biotechnol. 2006 Jun;17(3):250-5
16701993
Mol Syst Biol. 2009;5:320
19888215
Int J Syst Evol Microbiol. 2010 Apr;60(Pt 4):737-748
19656941
Saline Syst. 2008 Sep 15;4:14
18793408
Microbiol Mol Biol Rev. 1998 Jun;62(2):504-44
9618450
BMC Bioinformatics. 2010 Apr 29;11:213
20426874
Nucleic Acids Res. 2005 Mar 03;33(4):1399-409
15745999
J Appl Microbiol. 2006;100(1):98-107
16405689
Brief Bioinform. 2006 Jun;7(2):140-50
16772264
Metab Eng. 2008 Sep;10(5):227-33
18611443
Biotechnol Prog. 1999 May-Jun;15(3):296-303
10356246
FEMS Microbiol Rev. 2009 Jan;33(1):164-90
19067749