title: Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production.
abstract: BACKGROUND
  The bioethanol production system used in Brazil is based on the fermentation of sucrose from sugarcane feedstock by highly adapted strains of the yeast Saccharomyces cerevisiae. Bacterial contaminants present in the distillery environment often produce yeast-bacteria cellular co-aggregation particles that resemble yeast-yeast cell adhesion (flocculation). The formation of such particles is undesirable because it slows the fermentation kinetics and reduces the overall bioethanol yield.
  
  
  RESULTS
  In this study, we investigated the molecular physiology of one of the main S. cerevisiae strains used in Brazilian bioethanol production, PE-2, under two contrasting conditions: typical fermentation, when most yeast cells are in suspension, and co-aggregated fermentation. The transcriptional profile of PE-2 was assessed by RNA-seq during industrial scale fed-batch fermentation. Comparative analysis between the two conditions revealed transcriptional profiles that were differentiated primarily by a deep gene repression in the co-aggregated samples. The data also indicated that Lactobacillus fermentum was likely the main bacterial species responsible for cellular co-aggregation and for the high levels of organic acids detected in the samples.
  
  
  CONCLUSIONS
  Here, we report the high-resolution gene expression profiling of strain PE-2 during industrial-scale fermentations and the transcriptional reprograming observed under co-aggregation conditions. This dataset constitutes an important resource that can provide support for further development of this key yeast biocatalyst.
authors: Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. osmar@lge.ibi.unicamp.br.|Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA. osmar@lge.ibi.unicamp.br.
authors: Osmar V
authors: OV
authors: Carvalho-Netto
authors: Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. mcarazzo@lge.ibi.unicamp.br.
authors: Marcelo F
authors: MF
authors: Carazzolle
authors: Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. luciana.mofatto@gmail.com.
authors: Luciana S
authors: LS
authors: Mofatto
authors: Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. paulo@lge.ibi.unicamp.br.
authors: Paulo J P L
authors: PJ
authors: Teixeira
authors: Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. melfontes@gmail.com.
authors: Melline F
authors: MF
authors: Noronha
authors: Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. luige_7@hotmail.com.
authors: Luige A L
authors: LA
authors: Calderón
authors: Department of Genetics, University of North Carolina, Chapel Hill, NC, USA. Piotr_Mieczkowski@med.unc.edu.
authors: Piotr A
authors: PA
authors: Mieczkowski
authors: Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA. lucas.argueso@colostate.edu.
authors: Juan Lucas
authors: JL
authors: Argueso
authors: Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. goncalo@unicamp.br.
authors: Gonçalo A G
authors: GA
authors: Pereira
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D018533:Biomass; D001938:Brazil; D000431:Ethanol / Q000378:metabolism*; D005285:Fermentation; D005427:Flocculation; D020869:Gene Expression Profiling; D063990:Gene Ontology; D005838:Genotype; D007218:Industrial Microbiology / Q000379:methods; D007700:Kinetics; D056265:Microbial Interactions; D009154:Mutation; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D031786:Saccharum / Q000378:metabolism
chemical_list: D000431:Ethanol
references: Microbiology (Reading). 2001 Oct;147(Pt 10):2635-2642
references: 11577142
references: Genomics. 2010 Nov;96(5):259-65
references: 20688152
references: Nature. 1986 Feb 20-26;319(6055):689-93
references: 3005867
references: Curr Genet. 1996 May;29(6):511-5
references: 8662189
references: Appl Environ Microbiol. 2003 Oct;69(10):5855-63
references: 14532035
references: FEMS Yeast Res. 2006 Sep;6(6):924-36
references: 16911514
references: Genome Res. 2009 Dec;19(12):2258-70
references: 19812109
references: Mol Microbiol. 2006 Apr;60(1):5-15
references: 16556216
references: J Biol Chem. 1998 Oct 9;273(41):26836-43
references: 9756928
references: J Appl Microbiol. 2011 Jan;110(1):1-18
references: 21114594
references: OMICS. 2010 Oct;14(5):587-601
references: 20955010
references: J Biotechnol. 2013 Dec;168(4):701-9
references: 23994268
references: J Ind Microbiol Biotechnol. 2001 Mar;26(3):171-7
references: 11420658
references: Curr Protoc Mol Biol. 2001 May;Chapter 13:Unit13.12
references: 18265096
references: EMBO J. 2004 Jan 14;23(1):127-37
references: 14685262
references: Appl Microbiol Biotechnol. 2011 Sep;91(5):1267-75
references: 21735264
references: Appl Environ Microbiol. 2009 Apr;75(8):2320-5
references: 19251894
references: Biotechnol Appl Biochem. 2014 Jan-Feb;61(1):40-4
references: 23772864
references: J Biol Chem. 2000 Oct 20;275(42):32611-6
references: 10921921
references: Appl Environ Microbiol. 1997 Aug;63(8):3233-41
references: 9251210
references: Nucleic Acids Res. 2007;35(21):7188-96
references: 17947321
references: Yeast. 2002 Oct;19(14):1261-76
references: 12271461
references: FEMS Microbiol Rev. 1997 Nov;21(3):231-41
references: 9451815
references: Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9374-8
references: 10430950
references: J Bacteriol. 1998 Nov;180(21):5718-26
references: 9791124
references: Bioinformatics. 2008 Mar 1;24(5):713-4
references: 18227114
references: BMC Microbiol. 2010 Nov 23;10:298
references: 21092306
references: Biochem Biophys Res Commun. 2012 Mar 23;419(4):652-5
references: 22382028
references: World J Microbiol Biotechnol. 1994 Nov;10(6):697-9
references: 24421199
references: Braz J Microbiol. 2014 Jan 15;44(3):665-71
references: 24516432
references: Bioinformatics. 2010 Jan 1;26(1):136-8
references: 19855105
references: Appl Environ Microbiol. 2002 Apr;68(4):1616-23
references: 11916676
references: Bioinformatics. 2003 Sep 22;19(14):1787-99
references: 14512350
references: Yeast. 1997 Feb;13(2):127-37
references: 9046094
references: Nat Methods. 2008 Jul;5(7):621-8
references: 18516045
references: FEMS Microbiol Rev. 2001 Jan;25(1):15-37
references: 11152939
references: Mol Biol Cell. 2002 Aug;13(8):2598-606
references: 12181332
references: Mol Microbiol. 2001 Feb;39(3):533-41
references: 11169096
references: Microb Cell Fact. 2010 Oct 25;9:79
references: 20973990
references: J Bacteriol. 2005 Sep;187(17):6128-36
references: 16109954
references: J Biol Chem. 2003 Dec 12;278(50):49920-8
references: 14514673
references: Methods. 2001 Dec;25(4):402-8
references: 11846609
references: FEMS Yeast Res. 2008 Nov;8(7):1155-63
references: 18752628
references: Appl Biochem Biotechnol. 2006 Mar;131(1-3):795-807
references: 18563655
references: Antonie Van Leeuwenhoek. 2005 Jul;88(1):13-23
references: 15928973
references: Biosci Biotechnol Biochem. 2012;76(2):326-30
references: 22313775
references: Biochem Biophys Res Commun. 2005 Nov 11;337(1):95-103
references: 16176797
references: FEMS Microbiol Lett. 1996 Aug 1;141(2-3):207-12
references: 8768524
references: FEMS Yeast Res. 2007 Sep;7(6):819-33
references: 17484738
references: FEMS Yeast Res. 2009 Dec;9(8):1123-36
references: 19566685
references: Genome Res. 2009 Dec;19(12):2271-8
references: 19897511
references: Appl Environ Microbiol. 2008 Sep;74(18):5759-68
references: 18676708