Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation

Applied and Environmental Microbiology

Volumn 79, Issue 23, 2013, Pages 7325-7333

  Aslankoohi, Elham ^a,b   Zhu, Bo ^a,b   Rezaei, Mohammad Naser ^c   Voordeckers, Karin ^a,b   Maeyer, Dries De ^b   Marchal, Kathleen ^b   Dornez, Emmie ^c   Courtin, Christophe M ^c   Verstrepen, Kevin J ^a,b  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c LEUVEN FOOD SCIENCE AND NUTRITION RESEARCH CENTRE LFORCE   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID METABOLISM; DIFFERENTIALLY EXPRESSED GENE; EXPRESSION PATTERNS; FERMENTATION CAPACITY; GENETIC BACKGROUNDS; INDUSTRIAL PROCESSS; SACCHAROMYCES CEREVISIAE STRAINS; SOLID-STATE PROCESS;

AMINO ACIDS; GENE EXPRESSION; GLYCEROL; OSMOSIS; PHYSIOLOGY; YEAST;

FERMENTATION;

AMINO ACID; CELL ORGANELLE; FERMENTATION; GENE EXPRESSION; GENETIC ANALYSIS; METABOLISM; OSMOSIS; PHYSIOLOGY; YEAST;

TRANSCRIPTOME;

ARTICLE; BREAD; FERMENTATION; GENETICS; METABOLISM; MICROBIOLOGY; PHYSIOLOGICAL STRESS; SACCHAROMYCES CEREVISIAE;

BREAD; FERMENTATION; METABOLIC NETWORKS AND PATHWAYS; SACCHAROMYCES CEREVISIAE; STRESS, PHYSIOLOGICAL; TRANSCRIPTOME;

EID: 84888246933     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02649-13     Document Type: Article

References (66)

1. Pandey A. 1992. Recent process developments in solid-state fermentation. Process Biochem. 27:109-117.
2. Pandey A, Soccol CR, Rodriguez-Leon J, Nigam P. 2001. Solid-state fermentation in biotechnology: fundamentals and applications, 1st ed. Asiatech Publishers, New Delhi, India.
3. Pandey A, Selvakumar P, Soccol CR, Nigam P. 1999. Solid state fermentation for the production of industrial enzymes. Curr. Sci. 77:149-162.
4. Selvakumar P, Ashakumary L, Pandey A. 1998. Biosynthesis of glucoamylase from Aspergillus niger by solid-state fermentation using tea waste as the basis of a solid substrate. Bioresour. Technol. 65:83-85.
5. Cen P, Xia L. 1999. Production of cellulase by solid-state fermentation, p 69-92. In Scheper T, Tsao GT (ed), Recent progress in bioconversion of lignocellulosics. Springer, Berlin, Germany.
6. Singh-Nee Nigam P, Singh D. 1996. Processing of agricultural wastes in solid state fermentation for microbial protein production. J. Sci. Ind. Res. 55:373-380.
7. Robinson T, Singh D, Nigam P. 2001. Solid-state fermentation: a promising microbial technology for secondary metabolite production. Appl. Microbiol. Biotechnol. 55:284-289.
8. Mohanty SK, Behera S, Swain MR, Ray RC. 2009. Bioethanol production from mahula (Madhuca latifolia L.) flowers by solid-state fermentation. Appl. Energy 86:640-644.
9. Rodríguez L, Toro M, Vazquez F, Correa-Daneri M, Gouiric S, Vallejo M. 2010. Bioethanol production from grape and sugar beet pomaces by solid-state fermentation. Int. J. Hydrogen Energy 35:5914-5917.
10. Mazaheri D, Shojaosadati SA, Mousavi SM, Hejazi P, Saharkhiz S. 2012. Bioethanol production from carob pods by solid-state fermentation with Zymomonas mobilis. Appl. Energy 99:372-378.
11. Hölker U, Höfer M, Lenz J. 2004. Biotechnological advantages of laboratory-scale solid-state fermentation with fungi. Appl. Microbiol. Biotechnol. 64:175-186.
12. Pandey A, Soccol CR, Mitchell D. 2000. New developments in solid state fermentation. I. Bioprocesses and products. Process Biochem. 35:1153-1169.
13. Pandey A, Ashakumary L, Selvakumar P, Vijayalakshmi K. 1994. Influence of water activity on growth and activity of Aspergillus niger for glycoamylase production in solid-state fermentation. World J. Microbiol. Biotechnol. 10:485-486.
14. López-Calleja A, Cuadra T, Barrios-González J, Fierro F, Fernández F. 2012. Solid-state and submerged fermentations show different gene expression profiles in cephalosporin C production by Acremonium chrysogenum. J. Mol. Microbiol. Biotechnol. 22:126-134.
15. Backhus LE, DeRisi J, Brown PO, Bisson LF. 2001. Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions. FEMS Yeast Res. 1:111-125.
16. Pérez-Torrado R, Panadero J, Hernández-López MJ, Prieto JA, Randez-Gil F. 2010. Global expression studies in baker's yeast reveal target genes for the improvement of industrially-relevant traits: the cases of CAF16 and ORC2. Microb. Cell Fact. 9:56. doi:10.1186/1475-2859-9-56.
17. Cholet O, Hénaut A, Casaregola S, Bonnarme P. 2007. Gene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose. Appl. Environ. Microbiol. 73:2561-2570.
18. James T, Campbell S, Donnelly D, Bond U. 2003. Transcription profile of brewery yeast under fermentation conditions. J. Appl. Microbiol. 94:432-448.
19. Olesen K, Felding T, Gjermansen C, Hansen J. 2002. The dynamics of the Saccharomyces carlsbergensis brewing yeast transcriptome during a production-scale lager beer fermentation. FEMS Yeast Res. 2:563-573.
20. Marks VD, Merwe GK, Vuuren HJ. 2003. Transcriptional profiling of wine yeast in fermenting grape juice: regulatory effect of diammonium phosphate. FEMS Yeast Res. 3:269-287.
21. Rossignol T, Dulau L, Julien A, Blondin B. 2003. Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation. Yeast 20:1369-1385.
22. Zuzuarregui A, Olmo M. 2004. Expression of stress response genes in wine strains with different fermentative behavior. FEMS Yeast Res. 4:699-710.
23. Tanaka F, Ando A, Nakamura T, Takagi H, Shima J. 2006. Functional genomic analysis of commercial baker's yeast during initial stages of model dough-fermentation. Food Microbiol. 23:717-728.
24. Van Dijck P, Colavizza D, Smet P, Thevelein JM. 1995. Differential importance of trehalose in stress resistance in fermenting and nonfermenting Saccharomyces cerevisiae cells. Appl. Environ. Microbiol. 61:109-115.
25. Versele M, Thevelein JM, Van Dijck P. 2004. The high general stress resistance of the Saccharomyces cerevisiae fil1 adenylate cyclase mutant (Cyr1Lys1682) is only partially dependent on trehalose, Hsp104 and overexpression of Msn2/4-regulated genes. Yeast 21:75-86.
26. Verstrepen KJ, Iserentant D, Malcorps P, Derdelinckx G, Van Dijck P, Winderickx J, Pretorius IS, Thevelein JM, Delvaux FR. 2004. Glucose and sucrose: hazardous fast-food for industrial yeast? Trends Biotechnol. 22:531-537.
27. Remize F, Cambon B, Barnavon L, Dequin S. 2003. Glycerol formation during wine fermentation is mainly linked to Gpd1p and is only partially controlled by the HOG pathway. Yeast 20:1243-1253.
28. Legras JL, Karst F. 2003. Optimisation of interdelta analysis for Saccharomyces cerevisiae strain characterisation. FEMS Microbiol. Lett. 221:249-255.
29. Abelson JN, Simon MI, Guthrie C, Fink GR (ed). 2004. Guide to yeast genetics and molecular biology. Elsevier, London, United Kingdom.
30. Amberg DC, Burke DJ, Strathern JN. 2005. Methods in yeast genetics: a Cold Spring Harbor Laboratory course manual, 2005 ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. Shogren M, Finney K. 1984. Bread-making test for 10 grams of flour. Cereal Chem. 61:418-423.
32. Panadero J, Randez-Gil F, Prieto JA. 2005. Validation of a flour-free model dough system for throughput studies of baker's yeast. Appl. Environ. Microbiol. 71:1142-1147.
33. Zhou X, Ren L, Meng Q, Li Y, Yu Y, Yu J. 2010. The next-generation sequencing technology and application. Protein Cell 1:520-536.
34. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111.
35. Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D. 2013. Using Tablet for visual exploration of secondgeneration sequencing data. Brief. Bioinformatics 14:193-202.
36. Trapnell C, Roberts A, GoffL, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7:562-578.
37. Liu T, Lin N, Shi N, Zhang B. 2009. Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. BMC Bioinformatics 10:146. doi:10.1186/1471-2105-10-146.
38. Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140.
39. Dennis G, Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. 2003. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 4:P3. doi:10.1186/gb-2003-4-5-p3.
40. Voordeckers K, De Maeyer D, Zande E, Vinces MD, Meert W, Cloots L, Ryan O, Marchal K, Verstrepen KJ. 2012. Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology. Mol. Microbiol. 86:225-239.
41. Yeang C-H, Ideker T, Jaakkola T. 2004. Physical network models. J. Comput. Biol. 11:243-262.
42. Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR. 2009. Bridging highthroughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat. Genet. 41:316-323.
43. Pu S, Wong J, Turner B, Cho E, Wodak SJ. 2009. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 37:825-831.
44. De Maeyer D, Renkens J, Cloots L, De Raedt L, Marchal K. 2013. PheNetic: network-based interpretation of unstructured gene lists in E. coli. Mol. Biosyst. 9:1594-1603.
45. Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T. 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431-432.
46. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman W-H, Pagès F, Trajanoski Z, Galon J. 2009. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091-1093.
47. Maere S, Heymans K, Kuiper M. 2005. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448-3449.
48. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Stat. Methodol. 57:289-300.
49. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. 2000. Gene ontology: tool for the unification of biology. Nat. Genet. 25:25-29.
50. Gustin MC, Albertyn J, Alexander M, Davenport K. 1998. MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 62:1264-1300.
51. Hohmann S. 2002. Osmotic stress signaling and osmoadaptation in yeasts. Microbiol. Mol. Biol. Rev. 66:300-372.
52. Welsh DT. 2000. Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate. FEMS Microbiol. Rev. 24:263-290.
53. Ruijter GJ, Visser J, Rinzema A. 2004. Polyol accumulation by Aspergillus oryzae at low water activity in solid-state fermentation. Microbiology 150:1095-1101.
54. Kets E, Teunissen P, De Bont J. 1996. Effect of compatible solutes on survival of lactic acid bacteria subjected to drying. Appl. Environ. Microbiol. 62:259-261.
55. Velasco I, Tenreiro S, Calderon IL, André B. 2004. Saccharomyces cerevisiae Aqr1 is an internal-membrane transporter involved in excretion of amino acids. Eukaryot. Cell 3:1492-1503.
56. Grandbastien M-A, Audeon C, Bonnivard E, Casacuberta J, Chalhoub B, Costa A-P, Le Q, Melayah D, Petit M, Poncet C. 2005. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet. Genome Res. 110:229-241.
57. Lesage P, Todeschini A. 2005. Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet. Genome Res. 110:70-90.
58. Oliver KR, Greene WK. 2009. Transposable elements: powerful facilitators of evolution. Bioessays 31:703-714.
59. McClintock B. 1984. The significance of responses of the genome to challenge. Science 226:792-801.
60. Uesono Y, Toh-e A. 2002. Transient inhibition of translation initiation by osmotic stress. J. Biol. Chem. 277:13848-13855.
61. Rep M, Krantz M, Thevelein JM, Hohmann S. 2000. The transcriptional response of Saccharomyces cerevisiae to osmotic shock: Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J. Biol. Chem. 275:8290-8300.
62. Alexandre H, Ansanay-Galeote V, Dequin S, Blondin B. 2001. Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett. 498:98-103.
63. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241.
64. Brewster JL, de Valoir T, Dwyer ND, Winter E, Gustin MC. 1993. An osmosensing signal transduction pathway in yeast. Science 259:1760-1763.
65. Alejandro-Osorio AL, Huebert DJ, Porcaro DT, Sonntag ME, Nillasithanukroh S, Will JL, Gasch AP. 2009. The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol. 10:R57. doi:10.1186/gb-2009-10-5-r57.
66. Shivaswamy S, Iyer VR. 2008. Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response. Mol. Cell. Biol. 28:2221-2234.