title: Global features of gene expression on the proteome and transcriptome levels in S. coelicolor during germination.
abstract: Streptomycetes have been studied mostly as producers of secondary metabolites, while the transition from dormant spores to an exponentially growing culture has largely been ignored. Here, we focus on a comparative analysis of fluorescently and radioactively labeled proteome and microarray acquired transcriptome expressed during the germination of Streptomyces coelicolor. The time-dynamics is considered, starting from dormant spores through 5.5 hours of growth with 13 time points. Time series of the gene expressions were analyzed using correlation, principal components analysis and an analysis of coding genes utilization. Principal component analysis was used to identify principal kinetic trends in gene expression and the corresponding genes driving S. coelicolor germination. In contrast with the correlation analysis, global trends in the gene/protein expression reflected by the first principal components showed that the prominent patterns in both the protein and the mRNA domains are surprisingly well correlated. Analysis of the number of expressed genes identified functional groups activated during different time intervals of the germination.
authors.affiliation: Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
authors.forename: Eva
authors.initials: E
authors.lastname: Strakova
authors.forename: Jan
authors.initials: J
authors.lastname: Bobek
authors.forename: Alice
authors.initials: A
authors.lastname: Zikova
authors.forename: Jiri
authors.initials: J
authors.lastname: Vohradsky
mesh_terms: D004734:Energy Metabolism / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D053858:Metabolic Networks and Pathways; D010641:Phenotype; D025341:Principal Component Analysis; D020543:Proteome; D013171:Spores, Bacterial / Q000235:genetics* / Q000378:metabolism*; D048372:Streptomyces coelicolor / Q000235:genetics* / Q000378:metabolism* / Q000648:ultrastructure; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome
chemical_list: D020543:Proteome
references.citation: Biochem Biophys Res Commun. 2000 Feb 16;268(2):282-8
references.pmid: 10679194
references.citation: Can J Microbiol. 1993 Apr;39(4):377-83
references.pmid: 8500009
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):207-10
references.pmid: 11752295
references.citation: Mol Microbiol. 2012 Jul;85(2):326-44
references.pmid: 22651816
references.citation: PLoS One. 2008 May 07;3(5):e2097
references.pmid: 18461186
references.citation: EMBO J. 1999 Aug 2;18(15):4292-8
references.pmid: 10428967
references.citation: Proteomics. 2003 Oct;3(10):1912-9
references.pmid: 14625853
references.citation: FEBS Lett. 2009 Dec 17;583(24):3966-73
references.pmid: 19850042
references.citation: Mol Syst Biol. 2007;3:79
references.pmid: 17299416
references.citation: Mol Cell Proteomics. 2002 Apr;1(4):323-33
references.pmid: 12096114
references.citation: Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8409-14
references.pmid: 10890920
references.citation: Mol Microbiol. 2008 Jul;69(1):42-54
references.pmid: 18433449
references.citation: Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18371-6
references.pmid: 18003902
references.citation: Folia Microbiol (Praha). 1977;22(4):252-61
references.pmid: 892668
references.citation: Biochem Biophys Res Commun. 2002 Nov 29;299(2):335-42
references.pmid: 12437991
references.citation: Proteomics. 2004 Dec;4(12):3864-80
references.pmid: 15378695
references.citation: J Proteome Res. 2013 Jan 4;12(1):525-36
references.pmid: 23181467
references.citation: J Bacteriol. 2006 Sep;188(17):6269-76
references.pmid: 16923894
references.citation: Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1693-8
references.pmid: 11172013
references.citation: Nature. 2004 Feb 26;427(6977):839-43
references.pmid: 14985762
references.citation: J Bacteriol. 2010 Nov;192(21):5674-81
references.pmid: 20817765
references.citation: EMBO J. 1998 Oct 1;17(19):5776-82
references.pmid: 9755177
references.citation: Proteomics. 2007 Nov;7(21):3853-66
references.pmid: 17960737
references.citation: Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3351-6
references.pmid: 12631705
references.citation: Mol Cell Biol. 1999 Mar;19(3):1720-30
references.pmid: 10022859
references.citation: Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4209-14
references.pmid: 12646705
references.citation: Gene. 2012 Jan 15;492(1):71-80
references.pmid: 22108710
references.citation: J Bacteriol. 1999 Jan;181(1):204-11
references.pmid: 9864331
references.citation: Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10101-6
references.pmid: 10963673
references.citation: J Bacteriol. 2009 Nov;191(21):6501-12
references.pmid: 19717604
references.citation: Protein J. 2007 Jan;26(1):51-9
references.pmid: 17203395
references.citation: FASEB J. 2001 Sep;15(11):2054-6
references.pmid: 11511523
references.citation: Mol Biosyst. 2009 Dec;5(12):1512-26
references.pmid: 20023718