title: Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks.
abstract: The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. Transcriptomic, proteomic, and metabolomic data were integrated using two different strategies, one hypothesis free and the other hypothesis driven. A multistep hypothesis-free approach was applied to data from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified stage-specific functional networks of linked transcripts, proteins, and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data from three withering intervals, starting with subdata sets of transcripts, proteins, and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time and used these to select subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed.
authors.affiliation: Department of Biotechnology, University of Verona, Verona, Italy.
authors.forename: Anita
authors.initials: A
authors.lastname: Zamboni
authors.forename: Mariasole
authors.initials: M
authors.lastname: Di Carli
authors.forename: Flavia
authors.initials: F
authors.lastname: Guzzo
authors.forename: Matteo
authors.initials: M
authors.lastname: Stocchero
authors.forename: Sara
authors.initials: S
authors.lastname: Zenoni
authors.forename: Alberto
authors.initials: A
authors.lastname: Ferrarini
authors.forename: Paola
authors.initials: P
authors.lastname: Tononi
authors.forename: Ketti
authors.initials: K
authors.lastname: Toffali
authors.forename: Angiola
authors.initials: A
authors.lastname: Desiderio
authors.forename: Kathryn S
authors.initials: KS
authors.lastname: Lilley
authors.forename: M Enrico
authors.initials: ME
authors.lastname: Pè
authors.forename: Eugenio
authors.initials: E
authors.lastname: Benvenuto
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
authors.forename: Mario
authors.initials: M
authors.lastname: Pezzotti
mesh_terms: D015415:Biomarkers; D016000:Cluster Analysis; D005638:Fruit / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D023281:Genomics; D055432:Metabolomics; D020411:Oligonucleotide Array Sequence Analysis; D040901:Proteomics; D018749:RNA, Plant / Q000235:genetics; D027843:Vitis / Q000235:genetics*
chemical_list: D015415:Biomarkers; D018749:RNA, Plant
references.citation: J Exp Bot. 2008;59(10):2579-96
references.pmid: 18596111
references.citation: Plant Physiol. 2009 Nov;151(3):1513-30
references.pmid: 19741049
references.citation: Brief Funct Genomic Proteomic. 2008 Jul;7(4):239-48
references.pmid: 18579616
references.citation: J Agric Food Chem. 2004 Jul 14;52(14):4406-13
references.pmid: 15237944
references.citation: Plant Cell. 2008 Jul;20(7):1862-78
references.pmid: 18612100
references.citation: J Plant Physiol. 2007 Oct;164(10):1239-60
references.pmid: 17662502
references.citation: Plant J. 2009 Aug;59(4):612-21
references.pmid: 19392685
references.citation: Biosci Biotechnol Biochem. 2001 Jul;65(7):1652-5
references.pmid: 11515552
references.citation: Nature. 2007 Sep 27;449(7161):463-7
references.pmid: 17721507
references.citation: Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2221-6
references.pmid: 15647349
references.citation: Plant Physiol. 2007 Sep;145(1):87-97
references.pmid: 17616511
references.citation: BMC Genomics. 2007 Jun 21;8:187
references.pmid: 17584945
references.citation: Plant Physiol. 1991 Oct;97(2):844-6
references.pmid: 16668481
references.citation: J Virol Methods. 1987 Sep;17(3-4):277-85
references.pmid: 2824545
references.citation: J Exp Bot. 2008;59(15):4145-59
references.pmid: 19010774
references.citation: Annu Rev Plant Biol. 2010;61:463-89
references.pmid: 19152489
references.citation: Plant Physiol. 2009 Feb;149(2):1028-41
references.pmid: 19098092
references.citation: Phytopathology. 1999 Apr;89(4):298-302
references.pmid: 18944774
references.citation: Plant Physiol Biochem. 2009 Jul;47(7):551-61
references.pmid: 19375343
references.citation: Traffic. 2003 Jan;4(1):6-12
references.pmid: 12535270
references.citation: Planta. 2005 Nov;222(5):832-47
references.pmid: 16151847
references.citation: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15898-903
references.pmid: 12456878
references.citation: Bioessays. 2004 Jan;26(1):99-105
references.pmid: 14696046
references.citation: C R Biol. 2008 Aug;331(8):569-78
references.pmid: 18606386
references.citation: Postepy Biochem. 2006;52(3):330-8
references.pmid: 17201069
references.citation: Proteomics. 2004 Jan;4(1):201-15
references.pmid: 14730682
references.citation: Plant Physiol. 2006 Jan;140(1):150-8
references.pmid: 16361521
references.citation: Plant Mol Biol. 2004 Feb;54(3):353-72
references.pmid: 15284492
references.citation: IUBMB Life. 2007 Apr-May;59(4-5):355-60
references.pmid: 17505975
references.citation: Development. 2006 Dec;133(23):4655-65
references.pmid: 17079274
references.citation: Methods Mol Biol. 1999;112:95-7
references.pmid: 10027232
references.citation: J Med Food. 2009 Jun;12(3):473-84
references.pmid: 19627194
references.citation: Plant Physiol. 1991 Jan;95(1):264-8
references.pmid: 16667962
references.citation: Sci STKE. 2006 Dec 05;2006(364):cm5
references.pmid: 17148786
references.citation: Plant Physiol. 2004 Sep;136(1):2579-86
references.pmid: 15375206
references.citation: Peptides. 2004 Jul;25(7):1215-22
references.pmid: 15245883
references.citation: J Proteome Res. 2009 Jan;8(1):199-210
references.pmid: 19053836
references.citation: Proteomics. 2007 Sep;7(17):3154-70
references.pmid: 17683049
references.citation: Plant Mol Biol. 1994 Oct;26(1):495-502
references.pmid: 7948897
references.citation: BMC Genomics. 2007 Nov 22;8:429
references.pmid: 18034876
references.citation: Plant J. 2007 Dec;52(6):1181-91
references.pmid: 17931352
references.citation: J Proteome Res. 2009 Feb;8(2):838-48
references.pmid: 19099506
references.citation: Plant Cell. 2004 Aug;16(8):2089-103
references.pmid: 15269332
references.citation: Biochem Biophys Res Commun. 2005 Jun 3;331(2):675-80
references.pmid: 15850811
references.citation: J Agric Food Chem. 2001 Nov;49(11):5531-6
references.pmid: 11714355
references.citation: Funct Integr Genomics. 2005 Jan;5(1):40-58
references.pmid: 15480888
references.citation: Plant Physiol. 2008 Apr;146(4):1721-37
references.pmid: 18305213
references.citation: Plant J. 2003 Jun;34(6):753-67
references.pmid: 12795696
references.citation: Proteomics. 2009 May;9(9):2503-28
references.pmid: 19343710
references.citation: J Agric Food Chem. 2009 Apr 8;57(7):2955-60
references.pmid: 19334762
references.citation: Plant Mol Biol. 2010 Apr;72(6):607-20
references.pmid: 20112051
references.citation: BMC Genomics. 2008 Aug 08;9:378
references.pmid: 18691399
references.citation: J Agric Food Chem. 2003 Aug 27;51(18):5488-92
references.pmid: 12926902
references.citation: Traffic. 2007 Jun;8(6):774-83
references.pmid: 17488289
references.citation: Anal Chem. 2008 Jan 1;80(1):115-22
references.pmid: 18027910
references.citation: J Biol Chem. 1995 Jul 28;270(30):18158-64
references.pmid: 7629128
references.citation: Plant Cell. 2005 Sep;17(9):2454-72
references.pmid: 16055636
references.citation: Plant Physiol. 2009 Aug;150(4):1648-55
references.pmid: 19420325
references.citation: FEBS Lett. 1995 Sep 4;371(2):195-8
references.pmid: 7672127
references.citation: Mol Plant. 2010 May;3(3):509-23
references.pmid: 20118183
references.citation: Traffic. 2002 Jan;3(1):50-60
references.pmid: 11872142
references.citation: Plant Signal Behav. 2008 Sep;3(9):626-32
references.pmid: 19513253
references.citation: Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):658-63
references.pmid: 19124768
references.citation: Plant Physiol Biochem. 2007 Aug;45(8):521-34
references.pmid: 17560114
references.citation: Curr Biol. 2009 Dec 15;19(23):2031-6
references.pmid: 19913422
references.citation: J Agric Food Chem. 2006 Oct 4;54(20):7692-702
references.pmid: 17002441
references.citation: J Exp Bot. 2008;59(11):2979-90
references.pmid: 18550598
references.citation: J Cell Sci. 2009 Mar 1;122(Pt 5):587-93
references.pmid: 19225125
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Curr Opin Plant Biol. 2002 Dec;5(6):494-501
references.pmid: 12393011
references.citation: Phytochemistry. 2009 Jul-Aug;70(11-12):1329-44
references.pmid: 19762054
references.citation: Science. 2002 Oct 25;298(5594):763-4
references.pmid: 12399572
references.citation: Planta. 2001 Dec;214(2):257-64
references.pmid: 11800390
references.citation: Nucleic Acids Res. 2003 Jun 15;31(12):3057-62
references.pmid: 12799432
references.citation: BMC Genomics. 2007 Nov 22;8:428
references.pmid: 18034875
references.citation: J Biochem. 1999 May;125(5):899-903
references.pmid: 10220581
references.citation: Phytochemistry. 2002 Jul;60(6):551-65
references.pmid: 12126701
references.citation: Nat Prod Commun. 2009 May;4(5):611-34
references.pmid: 19445314
references.citation: PLoS One. 2009 Dec 21;4(12):e8365
references.pmid: 20027228
references.citation: BMC Evol Biol. 2009 Aug 03;9:183
references.pmid: 19650916
references.citation: Rapid Commun Mass Spectrom. 2008 Oct;22(20):3089-99
references.pmid: 18819110
references.citation: Plant Cell Physiol. 2000 Nov;41(11):1279-85
references.pmid: 11092914
references.citation: BMC Plant Biol. 2008 Jul 22;8:83
references.pmid: 18647406
references.citation: Methods. 2003 Dec;31(4):265-73
references.pmid: 14597310
references.citation: Mol Cell Proteomics. 2008 Jan;7(1):88-107
references.pmid: 17921517
references.citation: Science. 2009 Oct 2;326(5949):53-4
references.pmid: 19797647
references.citation: FEBS Lett. 1998 Feb 6;422(3):400-2
references.pmid: 9498825
references.citation: Biochemistry. 1996 Feb 13;35(6):1820-8
references.pmid: 8639663
references.citation: J Agric Food Chem. 2006 May 3;54(9):3334-40
references.pmid: 16637693