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UNIVERSIDAD DE ALCALÁ Desarrollo De Nuevos Marcadores Genómicos Para Estudios De Biodiversidad En Fotobiontes Liquénicos

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UNIVERSIDAD DE ALCALÁ Desarrollo De Nuevos Marcadores Genómicos Para Estudios De Biodiversidad En Fotobiontes Liquénicos UNIVERSIDAD DE ALCALÁ Departamento de Ciencias de la Vida TESIS DOCTORAL Desarrollo de nuevos marcadores genómicos para estudios de biodiversidad en fotobiontes liquénicos. Microalgas eucarióticas como fuente de recursos de utilidad biotecnológica Alicia del Hoyo Pérez Alcalá de Henares, 2014 UNIVERSIDAD DE ALCALÁ Departamento de Ciencias de la Vida TESIS DOCTORAL Desarrollo de nuevos marcadores genómicos para estudios de biodiversidad en fotobiontes liquénicos. Microalgas eucarióticas como fuente de recursos de utilidad biotecnológica Memoria presentada en la Universidad de Alcalá por la Licenciada Alicia del Hoyo Pérez para optar al grado de Doctor en Biología Evolutiva y Biodiversidad. LEONARDO CASANO MAZZA, Profesor Titular del Departamento de Ciencias de la Vida de la Universidad de Alcalá, y EVA MARÍA DEL CAMPO LÓPEZ, Profesora Contratada Doctora del Departamento de Ciencias de la Vida de la Universidad de Alcalá, CERTIFICAN: Que la presente Memoria titulada “Desarrollo de nuevos marcadores genómicos para estudios de biodiversidad en fotobiontes liquénicos. Microalgas eucarióticas como fuente de recursos de utilidad biotecnológica” ha sido realizada por Dña. Alicia del Hoyo Pérez en el Departamento de Ciencias de la Vida de la Universidad de Alcalá, con nuestra inmediata dirección y autorizamos su presentación para que sea calificada como Tesis Doctoral. Alcalá de Henares, mayo de 2014 Fdo.: Dr. Leonardo Casano Mazza Fdo.: Dra. Eva Mª del Campo López GONZALO PÉREZ SUÁREZ, Director del Departamento de Ciencias de la Vida de la Universidad de Alcalá CERTIFICA: Que la presente Memoria titulada “Desarrollo de nuevos marcadores genómicos para estudios de biodiversidad en fotobiontes liquénicos. Microalgas eucarióticas como fuente de recursos de utilidad biotecnológica” ha sido realizada por Dña. Alicia del Hoyo Pérez en el Departamento de Ciencias de la Vida de la Universidad de Alcalá, y cumple todos los requisitos para su presentación como Tesis Doctoral. Alcalá de Henares, mayo 2014 Fdo.: Dr. Gonzalo Pérez Suárez Por fin hemos llegado al final de esta carrera y me gustaría agradecer a todas las personas que me han acompañado durante estos años. A mis directores de Tesis, los Dres. Eva Mª del Campo y Leonardo Casano. Son muchas cosas las que he aprendido de cada uno de vosotros. Gracias por los consejos aportados, siempre interesantes y ayudando en todo lo posible. El esfuerzo mereció la pena. A la Dra. Eva Barreno y el Dr. Francisco García. Gracias por esa foto tan bonita que forma parte de la portada. Sin duda los fotobiontes son bonitos. A los miembros del Dpto. de Ciencias de la Vida. En especial al Dr. Carlos Illana, por sus muchas conversaciones hablando de cine e intentando arreglar el mundo. A la Dra. Carmen Bartolomé, por sus consejos y su forma de ser (mira Carmen, ya lo he conseguido). A Fernando Flores, siempre dispuesto a ayudarme cuando le he necesitado. A otras personas que componen la Universidad y con la que he compartido conversaciones muy interesantes, especialmente Antonio, Rufino y mi amigo Txomin. Se aprenden muchas cosas con vosotros, seguid siendo como sois: auténticos. Txomin, ya sabes, quiero verte pronto hablando de carábidos. A mi familia, que siempre ha estado apoyándome en los momentos más difíciles de este proceso. Mamá, papá, simplemente gracias. Me habéis enseñado tantas cosas… Sois los mejores. A ti Loren, mi hermano, te debo tiempo que no he podido disfrutar contigo y mi pequeña Lucía… Todo eso cambiará. Y a mis abuelos Alicia y Jesús, por haberme cuidado desde pequeña y ser otros padres para mi. Sin duda soy una afortunada de poder disfrutaros. A todos mis amigos, pero de forma muy especial a Raquel, porque lo de compartir camino se agradece. Gracias por todo, las conversaciones, el apoyo, esos viajes cargadas de morteros, pipetas y fotobiontes… Estoy segura de que vamos a conseguir todo lo que nos propongamos, ya sabes, somos SD y eso se nota. Mucha suerte amiga con lo que te queda, que ya es mucho menos que cuando empezamos. Y a ti Jorge, por ayudarme siempre en todo lo que necesito. Porque cuando el pánico cunde allí estás tú para poner tranquilidad… Y porque despertar cada día a tu lado es un regalo. A Jorge Índice de abreviaturas Para facilitar la lectura de los capítulos, tablas, esquemas y figuras incluidas en esta memoria, a continuación se incluye una ordenación alfabética de las abreviaturas más utilizadas: aá Aminoácido ADN Ácido desoxirribonucleico ADNr ADN ribosomal ARN Ácido ribonucleico C Citosina c.a. Cifra aproximada ADNc ADN copia EDTA Ácido etilen diaminotetraacético G Guanina GR Glutatión reductasa GSSG Glutatión oxidado HE Homing Endonucleasa IC Índice de consistencia IPTG isopropil- -D-1-tiogalactopiranósido ITS Espaciadores transcritos internos Kb Kilobase KDa KiloDalton ML Máxima verosimilitud MP Máxima Parsimonia MTT Bromuro de 3-(4,5-dimetiltiazol-2-il)-2,5 difeniltetrazolio NJ Neighbor Joining nt Nucleótido ORF Open Reading Frame (marco de lectura abierta) Pb Pares de bases PCR Reacción en cadena de la polimerasa PF Peso fresco pI Punto isoeléctrico Pm Peso molecular PVPP Polivinilpolipirrolidona SOD Superóxido dismutasa Tm Temperatura de fusión U Unidades enzimáticas ufc Unidades formadoras de colonias X-Gal 5-bromo-4-cloro-3-indolil- -D-galactopiranósido Índice ÍNDICE RESUMEN ...................................................................................................................... 1 1. INTRODUCCIÓN ............................................................................................................ 3 1.1. LAS MICROALGAS ................................................................................................... 5 1.1.1. Las algas verdes (División Chlorophyta) .......................................................... 8 1.1.2. Análisis de la biodiversidad de algas verdes: código de barras molecular ...... 8 1.1.3. Problemas de clasificación en algas verdes ................................................... 11 1.1.4. Marcadores moleculares utilizados en algas verdes ..................................... 13 1.2. LAS ALGAS LIQUÉNICAS ........................................................................................ 14 1.2.1. Las algas verdes en el contexto de la simbiosis liquénica ............................. 14 1.2.2. Estudios moleculares y fisiológicos de la diversidad de algas liquénicas ...... 17 1.3. APLICACIONES DE LAS ALGAS VERDES. LAS ALGAS VERDES COMO FUENTE DE HOMING ENDONUCLEASAS (HEs) ............................................................................... 18 1.3.1. Principales aplicaciones prácticas .................................................................. 18 1.3.2. Características generales de las Homing Endonucleasas .............................. 19 1.3.3. Mecanismos de homing ................................................................................. 21 1.3.4. Familias de Homing Endonucleasas ............................................................... 23 1.3.5. Homing Endonucleasas de la familia LAGLIDADG ......................................... 25 1.3.6. Aplicabilidad práctica de las Homing Endonucleasas .................................... 26 1.3.7. Diversos intrones de tipo I codifican Homing Endonucleasas en algas verdes ................................................................................................................................. 30 1.3.8. Presencia de intrones de tipo I y Homing Endonucleasas en algas liquénicas ................................................................................................................................. 31 2. OBJETIVOS ................................................................................................................... 33 3. MATERIALES Y MÉTODOS ........................................................................................... 37 3.1. MATERIAL BIOLÓGICO .......................................................................................... 39 Índice 3.2. MÉTODOS ............................................................................................................. 39 3.2.1. Aislamiento de fotobiontes liquénicos .......................................................... 39 3.2.2. Cultivo de microalgas ..................................................................................... 40 3.2.3. Aislamiento de ADN total .............................................................................. 41 3.2.4. Diseño de cebadores ..................................................................................... 41 3.2.5. Amplificación por PCR del ADN aislado ......................................................... 42 3.2.6. Separación electroforética y purificación de productos de amplificación .... 43 3.2.7. Clonación de un fragmento del gen psbB de Coccomyxa sp. ........................ 43 3.2.7.1. Ligación del fragmento al vector y transformación de células de E.coli 43 3.2.7.2. Purificación del ADN plasmídico ............................................................. 44 3.2.8. Análisis bioinformático de secuencias de ADN y proteínas .......................... 45 3.2.8.1. Análisis filogenético y construcción de árboles ...................................... 45 3.2.8.2. Análisis bioinformático de proteínas ...................................................... 47 3.2.9. Análisis de parámetros fisiológicos ............................................................... 47 3.2.9.1. Determinación de pigmentos fotosintéticos .......................................... 47 3.2.9.2. Extracción
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