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Proteomic Approach to Flatfish Aquaculture, Study of The DEPARTMENT of BIOCHEMISTRY and MOLECULAR BIOLOGY Doctoral Program in Biochemistry and Molecular Biology "PROTEOMIC APPROACH TO FLATFISH AQUACULTURE. STUDY OF THE REPRODUCTIVE BIOLOGY OF SOLEA SENEGALENSIS." IGNASI FORNÉ i FERRER MAY, 2007 DEPARTMENT of BIOCHEMISTRY and MOLECULAR BIOLOGY Doctoral Program in Biochemistry and Molecular Biology Doctoral thesis presented by IGNASI FORNÉ FERRER to obtain the Ph.D. IN BIOCHEMISTRY AND MOLECULAR BIOLOGY This work has been carried out in the Proteomics Laboratory CSIC/UAB and in Oryzon Genomics under the supervision of Dr. Joaquín Abian and Dr. Joan Cerdà. Ph.D. candidate Ph.D. Supervisor IGNASI FORNÉ i FERRER Dr. JOAQUIN ABIAN MOÑUX CSIC Research Scientist Department Tutor Ph.D. Supervisor Dr. JAUME FARRÉS VICÉN Dr. JOAN CERDÀ LUQUE UAB Biochemistry and Molecular IRTA Research Scientist Biology Professor Barcelona, May 2007 Veles e vents han mos desigs complir, faent camins dubtosos per la mar. Mestre i ponent contra d'ells veig armar; xaloc, llevant, los deuen subvenir ab llurs amics lo grec e lo migjorn, fent humils precs al vent tramuntanal que en son bufar los sia parcial e que tots cinc complesquen mon retorn. Bullirà el mar com la cassola en forn, mudant color e l'estat natural, e mostrarà voler tota res mal que sobre si atur un punt al jorn. Grans e pocs peixs a recors correran e cercaran amagatalls secrets: fugint al mar, on són nodrits e fets, per gran remei en terra eixiran. Ausiàs March (Veles e vents) No importa el problema, no importa la solución, me quedo con lo poco que queda, entero en el corazón. Me gustan los problemas, no existe otra explicación. Esta sí es una dulce condena, una dulce rendición. Andrés Calamaro (Dulce condena) Agraïments En primer lloc agrair al Dr. Carlos Buesa i al Dr. Joaquin Abián la possibilitat de realitzar el treball de tesi doctoral conjuntament al Laboratori de Proteómica CSIC-UAB i a Oryzon Genomics, per la oportunitat que suposa combinar el dia a dia del creixement d’una empresa biotecnològica i la convivència en un entorn acadèmic de referència en espectrometria de masses i proteòmica. Al Dr. Joaquín Abián (de nou) i al Dr. Joan Cerdà per la direcció de la tesis i per la seva implicació personal, dedicació, suport i esforç en tot moment. A tota la gent que ha participat en el disseny i realització del projecte Pleurogene, en especial al Dr. Joan Cerdà per la coordinació general, i a la Dra. Tamara Maes per la direcció científica des d’Oryzon Genomics. Al Dr. Jaume Farrés per la tutoria d’aquest treball, per la seva col·laboració i disponibilitat en tot moment. A tota la gent que he conegut a Oryzon durant aquests gairebé quatre anys, especialment a la Maite del Hierro, per ser una persona i companya de laboratori excel·lent, per la seva responsabilitat i el seu humor (kapasao-i-yokezé!!); al Joaquin (darrer cop) per la seves dosis de moral, experiència i temps quan les coses anaven maldades; al Jaume Mercadé per la col·laboració en el darrer capítol i per les converses sobre cóm canviar el món; al Dr. Toni Espinosa per la seva col·laboració en el primer capítol i per estar sempre a punt per fer “unas risas”; a la Dra. Elisabet Rosell per la seva mà esquerra i l’optimisme que transmet; al Xavi Calvo pel seu ajut en l’apartat de microarrays i per cuidar-me la cadira durant les meves llargues absències; al Jaume, el Jordi, l’Elena, el Roger i el Ricard per compartir l’experiència de fer una tesi dins de la empresa (ànims, que hi ha una llum al final!!); i a tots els que heu participat en les tertúlies després de dinar, en una sessió de youtube o senzillament amb un somriure en un mal dia. Als companys del Laboratori de Proteómica CSIC-UAB que ja hi eren quan vaig arribar, en especial a la Dra. Montse Carrascal pel temps i les energies dedicades (si hay que hacerlo, se hace…), i a la Dra. Carme Quero pels primers temps al lab; als que han passat deixant petjada, en especial al Miguel Trigo per la convivència al “zulo”, i als que Agraïments us quedeu i encara m’acolliu de bon grat quan vinc de visita: Marina, David, Rebeca, Vanesa i Cristina. Al Dr. Francesc Canals per facilitar-me l’ús del Laboratori de Proteómica de Vall d’Hebrón, a la Núria per les classes de Decyder i, junt amb la Cristina, per fer les hores de Decyder/Typhoon molt més amenes. Al Dr. Jaume Planas per la cessió dels resultats de microarrays del segon capítol. Al Miquel Daura de “Common Sense” pel disseny de la portada i del CD. A tots els que m’heu ajudat a créixer dins del món de la investigació en els diferents centres on he tingut la sort de treballar, en especial al Dr. Cándido Juarez del Departament d’Immunologia de l’Hospital de Sant Pau, per les primeres passes en el món de la proteómica. A tots els amics que heu col·laborat desinteressadament en el meu suport psicològic durant aquests anys, a la Cristina i al Miquel per la Vila del Pingüí (i per tantes altres coses…), a la Sónia i al Pedro per Madrids, Lisboas, París i Basileas, i a tots quatre per uns quants Munichs; al Jordi i al Natxo per estar sempre a punt; a la colla de l’ESM (ja sabeu qui sou…), per tant anys d’històries. Al meu germà Oriol per tots els moments junts a casa, pistes, pavellons, gimnasos, bars i festes majors: per ser com és. Als meus pares, Anna i Ernest, per educar-me i fer-me créixer amb generositat, convicció i amor, donant-me totes les oportunitats i les eines que m’han permès arribar fins aquí. A la meva dona Alexandra, per tenir les mides perfectes de “Cherry Blossom Girl”, de “Limón y Sal” i d’“Alegria”; i a la meva filla Paula pels moments únics que he viscut i espero viure. A totes dues, “I just want say “Hi” to the ones I love”. Table of Contents TOC Abbreviations Introduction…………………………………………………………………………………………… 1 I.1 Flatfish species…………………………………………………………………………… 1 I.1.1 Flatfish aquaculture………………………………………………………. 2 I.1.2 Teleost spermatogenesis………………………………………………… 3 I.1.3 Special features of Solea senegalensis spermatogenesis………….. 9 I.1.4 Steroid role during spermatogenesis and spermiation in teleosts…… 12 I.1.5 Hormone treatment approaches on flatfish spermatogenesis……….. 16 I.2 Proteomics………………………………………………………………………………… 17 I.2.1 Mass-spectrometry based proteomics…………………………………. 17 I.2.2 Differential expression analysis in proteomics………………………… 21 I.2.3 Annotation of DNA databases using peptidic ESTs…………………. 26 I.3 Applying proteomics to Solea senegalensis………………………………….............. 28 Objectives…………………………………………………………………………………………….. 29 About the Pleurogene Project: understanding the frame of this PhD work…………… 29 Chapter 1 De novo peptide sequencing of S. senegalensis larva and testis proteome using two-dimensional liquid chromatography coupled to tandem mass spectrometry…………………………………………………………………………….. 33 1.1 Materials and methods…………………………………………………………………. 35 1.1.1 Sample processing ………………………………………………………. 35 1.1.2 Two-dimensional LC MS-MS……………………………………………. 35 1.1.3 Data processing and refinement………………………………………... 39 1.2 Results…………………………………………………………………………………… 44 1.2.1 Two-dimensional LC, de novo sequencing and BLAST comparison.. 44 1.2.2 Methodological analysis: peptide charge distribution among 2-D LC.. 45 1.2.3 Biological analysis: GO charts………………………………………….. 45 1.3 Discussion………………………………………………………………………………. 52 1.3.1 Methodological analysis…………………………………………………. 52 1.3.2 Biological analysis………………………………………………………... 55 TOC Chapter 2 Proteomic analysis of differentially expressed proteins in wild and cultured Solea senegalensis during the spermatogenesis process…………………………………. 59 2.1 Materials and methods………………………………………………………………….. 60 2.1.1 Biological samples………………………………………………………… 60 2.1.2 Histological analysis………………………………………………………. 60 2.1.3 Protein extraction………………………………………………………….. 61 2.1.4 Two-dimensional electrophoresis……………………………………….. 62 2.1.5 Differential expression analysis and clustering………………………… 63 2.1.6 Determination of gel variation: Mr and pI variation……………………. 64 2.1.7 Determination of gel variation: Normalized volume variation………… 64 2.1.8 Protein identification………………………………………………………. 65 2.1.9 Bioinformatic analysis of MS/MS spectra………………………………. 66 2.1.10 Comparing sequenced peptides and identified proteins with S. senegalensis ESTs……………………………………………………….. 67 2.2 Results……………………………………………………………………………………. 69 2.2.1 Histological analysis………………………………………………………. 69 2.2.2 Two-dimensional electrophoresis……………………………………….. 69 2.2.3 Differential expression analysis and clustering………………………… 70 2.2.4 Mass spectrometry and bioinformatic analysis………………………… 88 2.2.5 Comparison of sequenced peptides and identified proteins with S. senegalensis ESTs……………………………………………………….. 97 2.3 Discussion……………………………………………………………………………….. 100 2.3.1 Gel Reproducibility………………………………………………………... 102 2.3.2 Expression analysis………………………………………………………. 103 2.3.3 Protein identification……………………………………………………… 106 2.3.4 Use of genomic ESTs for annotation cross-validation………………… 108 2.3.5 Biological implications of variations in testis proteome……………….. 112 2.3.6 Relationships between 2-D protein gel analysis and RNA microarray data in F0 ………………………………………………………………….. 119 Chapter 3 Effect of hormone treatments into testis proteome in cultured Solea senegalensis. Study by 2-D DIGE………………………………………………… 121 3.1 Materials and methods………………………………………………………………….. 122 3.1.1 Fish hormone treatments………………………………………………… 122 3.1.2 Biological samples………………………………………………………… 122 3.1.3 Histological analysis………………………………………………………. 123 3.1.4 Determination of sperm density and motility…………………………… 123 TOC 3.1.5 Protein extraction………………………………………………………… 124 3.1.6 Two-dimensional DIGE…………………………………………………. 124 3.1.7 Differential expression analysis and clustering………………………. 127 3.1.8 Protein identification…………………………………………………….. 128 3.1.9 Microarray analysis of testis transcriptome in hormone-treated fish… 128 3.2 Results…………………………………………………………………………………… 130 3.2.1 Effect of hormone treatments on spermatogenesis…………………… 130 3.2.2 Determination of GSI, sperm density and motility……………………... 131 3.2.3 Two-dimensional DIGE: self-to-self analysis…………………………… 131 3.2.4 Two-dimensional DIGE: evaluation experiment……………………….
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