title: Metabolic capabilities and systems fluctuations in Haloarcula marismortui revealed by integrative genomics and proteomics analyses.
abstract: The 1310 Haloarcula marismortui proteins identified from mid-log and late-log phase soluble and membrane proteomes were analyzed in metabolic and cellular process networks to predict the available systems and systems fluctuations upon environmental stresses. When the connected metabolic reactions with identified proteins were examined, the availability of a number of metabolic pathways and a highly connected amino acid metabolic network were revealed. Quantitative spectral count analyses suggested 300 or more proteins might have expression changes in late-log phase. Among these, integrative network analyses indicated approximately 106 were metabolic proteins that might have growth-phase dependent changes. Interestingly, a large proportion of proteins in affected biomodules had the same trend of changes in spectral counts. Disregard the magnitude of changes, we had successfully predicted and validated the expression changes of nine genes including the rimK, gltCP, rrnAC0132, and argC in lysine biosynthesis pathway which were downregulated in late-log phase. This study had not only revealed the expressed proteins but also the availability of biological systems in two growth phases, systems level changes in response to the stresses in late-log phase, cellular locations of identified proteins, and the likely regulated genes to facilitate further analyses in the postgenomic era.
authors: Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China.
authors: Lichieh Julie
authors: LJ
authors: Chu
authors: Hanyin
authors: H
authors: Yang
authors: Peiyin
authors: P
authors: Shih
authors: Yuchieh
authors: Y
authors: Kao
authors: Yihsuan Shannon
authors: YS
authors: Tsai
authors: Jinzhi
authors: J
authors: Chen
authors: Gueitang
authors: G
authors: Huang
authors: Rueyhung Roc
authors: RR
authors: Weng
authors: Ying Sonia
authors: YS
authors: Ting
authors: Xuefeng
authors: X
authors: Fang
authors: Priska D
authors: PD
authors: von Haller
authors: David R
authors: DR
authors: Goodlett
authors: Wailap Victor
authors: WV
authors: Ng
references: Proc Natl Acad Sci U S A. 1983 Apr;80(8):2201-5
references: 6300900
references: Anal Chem. 1995 Apr 15;67(8):1426-36
references: 7741214
references: Anal Chem. 2002 Oct 15;74(20):5383-92
references: 12403597
references: J Proteome Res. 2010 Feb 5;9(2):1138-43
references: 19938873
references: Genome Res. 2005 Oct;15(10):1336-43
references: 16169924
references: J Bacteriol. 1990 Dec;172(12):7065-70
references: 2123861
references: Rapid Commun Mass Spectrom. 2003;17(18):2093-8
references: 12955739
references: Bacteriol Rev. 1974 Sep;38(3):272-90
references: 4607500
references: Indian J Biochem Biophys. 1988 Dec;25(6):674-86
references: 3255682
references: J Biol Chem. 1985 Dec 5;260(28):15180-5
references: 3934156
references: Science. 1991 Feb 15;251(4995):767-73
references: 1990438
references: Nat Methods. 2007 Mar;4(3):207-14
references: 17327847
references: Methods Enzymol. 1974;31:667-78
references: 4418026
references: Mol Syst Biol. 2005;1:2005.0017
references: 16729052
references: J Biol Chem. 2006 Jul 21;281(29):20404-17
references: 16679316
references: J Bacteriol. 2004 Sep;186(18):6198-207
references: 15342590
references: Genomics. 2008 Jun;91(6):548-52; author reply 553-4
references: 18538726
references: Mol Cell Proteomics. 2003 Aug;2(8):506-24
references: 12872007
references: J Bacteriol. 2010 Sep;192(17):4528-9
references: 20601480
references: Nature. 2003 Mar 13;422(6928):198-207
references: 12634793
references: Annu Rev Biochem. 1989;58:173-94
references: 2673008
references: Extremophiles. 2008 Mar;12(2):177-96
references: 18278431
references: J Proteome Res. 2011 Mar 4;10(3):1170-8
references: 21158390
references: J Bacteriol. 1994 Sep;176(17):5505-12
references: 8071229
references: Adv Microb Physiol. 1977;15:85-120
references: 333878
references: Mol Syst Biol. 2009;5:282
references: 19536205
references: Saline Syst. 2010 Jun 22;6:7
references: 20569477
references: Science. 1996 Oct 25;274(5287):610-4
references: 8849452
references: Protein Sci. 1998 Mar;7(3):706-19
references: 9541403
references: Science. 1995 Oct 20;270(5235):467-70
references: 7569999
references: Nat Biotechnol. 2004 Nov;22(11):1459-66
references: 15529173
references: Mol Cell Proteomics. 2008 Dec;7(12):2373-85
references: 18644780
references: Mol Cell Proteomics. 2006 Jun;5(6):987-97
references: 16497792
references: Genome Res. 2004 Nov;14(11):2221-34
references: 15520287
references: Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12176-81
references: 11016950
references: J Mol Biol. 2001 Jan 19;305(3):567-80
references: 11152613
references: PLoS One. 2010 Mar 19;5(3):e9605
references: 20333302
references: Genome Res. 2001 Oct;11(10):1641-50
references: 11591641
references: Genome Res. 1998 Nov;8(11):1131-41
references: 9847077
references: Proc Natl Acad Sci U S A. 1982 Dec;79(23):7268-72
references: 6296826
references: Anal Chem. 2003 Sep 1;75(17):4646-58
references: 14632076
references: J Bacteriol. 2010 Nov;192(22):5866-73
references: 20802037
references: Genomics. 2008 Apr;91(4):335-46
references: 18313895
references: BMC Genomics. 2006 Jul 04;7:169
references: 16820047
references: Arch Microbiol. 2001 Jan;175(1):52-61
references: 11271421