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WINE YEAST: the CHALLENGE of LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013

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WINE YEAST: the CHALLENGE of LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. 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Tampoco se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR (framing). Esta reserva de derechos afecta tanto al contenido de la tesis como a sus resúmenes e índices. WARNING. Access to the contents of this doctoral thesis and its use must respect the rights of the author. It can be used for reference or private study, as well as research and learning activities or materials in the terms established by the 32nd article of the Spanish Consolidated Copyright Act (RDL 1/1996). Express and previous authorization of the author is required for any other uses. In any case, when using its content, full name of the author and title of the thesis must be clearly indicated. Reproduction or other forms of for profit use or public communication from outside TDX service is not allowed. Presentation of its content in a window or frame external to TDX (framing) is not authorized either. These rights affect both the content of the thesis and its abstracts and indexes. UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 Zoel Salvadó i Belart Wine yeast: The challenge of low temperature Doctoral Thesis supervised by Dr. José M. Guillamón Navarro & Dr. Ricardo Cordero Otero Departament de Bioquímica i Biotecnologia TARRAGONA 2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 Departament de Bioquímica i Biotecnologia C/Marcel·lí Domingo, s/n 43007 Tarragona Els sotasignats, Dr José Manuel Guillamón Navarro, Investigador Científico del Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC) y el Dr. Ricardo Cordero Otero, professor agregat del Departament de Bioquímica i Biotecnologia de la Universitat Rovira i Virgili FAN CONSTAR que el present treball, amb títol, Wine yeast: The challenge of low temperature. que presenta el Sr. Zoel Salvadó i Belart per a optar al Grau de Doctor per la Universitat Rovira i Virgili ha estat realitzat sota la nostra direcció, i que tots els resultats obtinguts són fruit dels experiments duts a terme per l’esmentat doctorand. I perquè se’n prengui coneixement i tingui els efectes que correspongui, signem aquesta certificació. Dr. José Manuel Guillamón Navarro Dr. Ricardo Cordero Otero UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 DECLARATION I, the undersigned, hereby declare that the work contained in this dissertation is my own original work and that I have not previously in its entirety or in part submitted it at any university for a degree. Zoel Salvadó I Belart Date UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 Index Preface 11 Introduction and outline of the thesis 13 Chapter 1: Temperature adaptation markedly determines evolution within the Saccharomyces genus 37 Chapter 2: Quantifying the individual effects of ethanol and temperature on the fitness advantage of Saccharomyces cerevisiae 63 Chapter 3: Proteomic evolution of a wine yeast during the first hours of fermentation 87 Chapter 4: Functional analysis to identify genes in wine yeast adaptation to low temperature fermentation 109 General discussion and perspectives 139 Conclusions 149 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 Preface Yeast has been used by humans for thousands of years, mainly for produce food products as beer, wine, bred and the like. This ancient empirical know-how was transmitted over the time during generations to handle all those biotechnological processes without knowing what or why those food products change their physical properties such as flavor, texture, consistency, longevity, etc. In XIV century first optical microscope was invented by Anton van Leeuwenhoek and whole new microscopic life forms were discovered allowing the microbiology and biotechnology to start as relevant sciences. A steady development of biological knowledge and science followed and start to unravel the know-why and know-what behind all those ancient biotechnological processes. Pioneers on these fields were eminent personalities such as Louis Pasteur, Robert Koch, and Alexander Fleming among many others. Nowadays modern biotechnology has become a complex science field in which convergence of various, previously distinct, biological disciplines occurs: microbiology, genetics, biochemistry, molecular biology, genetic engineering, etc. Yeast has played a central role on development of this new scientific field. Furthermore these microorganisms, and mainly the species Saccharomyces cerevisiae, has become a model organism of eukaryotic cell studies in modern biotechnology. In the last 30 years, explosion of genetic engineering and high throughput techniques like genomics, proteomics and metabolomics in combination with so-called classical techniques have produced a knowledge-based transition of traditional food products elaboration to high technological food production all over the world. Wine industry has been also involved in this technological revolution that encompasses all oenological practices from field to glass. One of the key points in wine production is the biocatalized reaction that transforms grape sugars (glucose and fructose) into ethanol and carbon dioxide. Yeasts are the main responsible of this phenomenon but also responsible of production of diverse secondary metabolites (glycerol, acetate, succinate, piruvate, and esters) that greatly contribute to the wine sensorial properties. Due to great impact of yeast to final wine quality, big efforts on wine biotechnology, in which this thesis may be included, have been dedicated to study yeast on winemaking process. 11 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 UNIVERSITAT ROVIRA I VIRGILI WINE YEAST: THE CHALLENGE OF LOW TEMPERATURE Zoel Salvadó Belart Dipòsit Legal: T.1304-2013 Introduction and outline of the thesis What are Saccharomyces yeasts? Yeasts are unicellular fungi widespread in natural world. They can be easily found in flowers, plant leaves, fruits, soil, etc. Yeasts are also found in animal skin or intestinal tracts of warm- blooded animals usually as innocuous flora but occasionally as a pathogen organism. However, for humanity yeasts have had a special relevance in human driven food production. Yeasts are true fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). Yeasts multiply as single cell that divides by budding (e.g. Saccharomyces) or direct fission division, (e.g. Schizosaccharomyces), or they may grow as simple irregular filaments (mycelium). Historically, taxonomy used morphological, reproductive and physiological characters to classify yeasts. This methodology was based mainly in binary characteristics with rapid evolution and
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