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Acknowledges FCUP 1 Molecular analysis of Nuclear Receptors in the Class Anthozoa (Cnidaria) ACKNOWLEDGES I thank Dr. Agostinho Antunes for give me the opportunity to be part of the Project PTDC/MAR/68106/2006 - “A modelação das vias de sinalização do ácido retinóico por contaminantes ambientais em teleósteos” and in Project PTDC/MAR/115199/2009 -"Estudo da modelação das vias de sinalização dos retinóides e das hormonas da tiróide, por disruptores endócrinos, em invertebrados"; for his support and advices. I am grateful to Barbara Frazão for her helps in the integration in the lab work and for share her knowledge about the protocols implemented; to Anoop Alex for his suggestions and discussions, which helped me to increase the knowledge about molecular techniques and to Cidália Gomes for her PCR recommendations and suggestions for the master thesis. I am grateful to all my lab mates of the molecular biology for the help in the handling of many tools and specially Pedro Leão, Joana Martins and Raquel Branco for their help in the TA cloning; to all my lab mates of the bioinformatics/phylogenetic for teach me about phylogenetic analysis. I thank Dr. Filipe Castro, Dr. Miguel Santos for their helpful suggestions and I acknowledge all team’s of the laboratories of CIIMAR where I was allowed to use their tools: ECOTOX, LETOX, LANUCE and specially the LEGE (Lab Ecotoxicology, Genomics and Evolution) where I developed all my work. I am also grateful to Vincent Laudet, Zdenek Kostrouch and Ann Tarrant, who answered by email to my doubts about their reports. FCUP 2 Molecular analysis of Nuclear Receptors in the Class Anthozoa (Cnidaria) ABSTRACT Nuclear receptors (NRs) are intracellular transcription factors which are restricted to metazoan organisms. Reduced data has been reported on the diversity of these receptors, especially in early metazoan lineages. Previous studies suggested lineage-specific diversification of several NR genes, such as the diversification of retinoid X receptor (RXR) gene within the Phylum Cnidaria (Reitzel and Tarrant, 2009). Currently, only a few sequences of NRs and/or RXR genes have been reported in Cnidaria, therefore six cnidarian species were analyzed in this study: Actinia equina, Actinia fragacea, Anthothoe sphyrodeta, Anemonia sulcata, Bunodactis verrucosa and Urticina felina. A combination of molecular approaches was used to assess RXR gene in the most basal cnidarian class, the Class Anthozoa. In addition, the amplification of other NRs from the NR2 family previously reported in this phylum was performed. We supported the hypothesis of RXR absence in anthozoans given the non-amplification of DBD fragments of the RXR in the target species. However, in Anemonia sulcata five partial NRs sequences were retrieved, such as the FTZ-F1, TR2/4 and COUPT-TF receptors. In Anthothoe spyrodeta, Bunodactis verrucosa, and Urticina felina, one fragment of TR2/4 was also obtained. Moreover, phylogenetic analysis using representative NRs reinforced the evidence that four A. sulcata sequences found encode also a COUPT-TF receptor, two TR2/4-like receptors and a NR with an inconclusive position within the NR2 family. A conclusion of this work is the need to increase the datasets and knowledge on the NRs existing in the phylum Cnidaria. Key words: nuclear receptor, RXR, Cnidaria, molecular analysis. RESUMO Os recetores nucleares (NRs) são fatores de transcrição intracelulares que são restritos aos metazoários. Poucos dados têm sido documentados acerca da sua diversidade, especialmente nos metazoários menos evoluídos. Artigos anteriores sugerem a diversificação específica de genes de NRs em determinados taxa, tal como a diversificação do gene RXR no filo Cnidária (Reitzel e Tarrant, 2009). Atualmente, poucas sequências de genes de NRs e/ou do gene RXR têm sido publicados em FCUP 3 Molecular analysis of Nuclear Receptors in the Class Anthozoa (Cnidaria) metazoários; pelo que neste estudo seis espécies de cnidários foram analisadas: Actinia equina, Actinia fragacea, Anthothoe sphyrodeta, Anemonia sulcata, Bunodactis verrucosa e Urticina felina. Uma combinação de metodologias moleculares foi usada para estudar o gene RXR na classe mais basal dos cnidários, a classe Anthozoa. Para além disso, foi realizada a amplificação de outros NRs da família NR2 anteriormente publicados em cnidários. Nós apoiamos a hipótese que defende a ausência do gene RXR nos antozoários, atendendo à não amplificação do fragmento do DBD do RXR nas espécies-alvo. Mas, na Anemonia sulcata foram obtidas sequências parciais de cinco NRs, nomeadamente dos recetores FTZ-F1, TR2/4 e COUPT-TF. Na espécie Anthothoe sphyrodeta, Bunodactis verrucosa, Urticina felina também foi amplificado um fragmento do TR2/4. A análise filogenética com NRs de taxa representativos reforçou o indício de que quatro sequências descobertas na A. sulcata codificam um recetor COUP-TF, dois recetores TR2/4 e um NR cuja classificação dentro da família NR2 é inconclusiva. Uma conclusão deste trabalho é a necessidade de aumentar os dados e o conhecimento acerca de NRs existentes no filo Cnidária. Palavras-chave: recetor nuclear, RXR, Cnidária, análise molecular. FCUP 4 Molecular analysis of Nuclear Receptors in the Class Anthozoa (Cnidaria) CONTENTS Acknowledges .................................................................................................... 1 Abstract .............................................................................................................. 2 Resumo .............................................................................................................. 2 Contents ............................................................................................................. 4 List of Abbreviations ........................................................................................... 6 List of Tables ...................................................................................................... 9 List of Figures ..................................................................................................... 9 Introduction....................................................................................................... 11 1. Signalling trough Nuclear Receptors (NRs) ........................................ 11 1.1. Signalling trough Retinoic Acid ........................................................... 13 1.1.1. Retinoic X Receptor (RXR): gene and protein .................................... 13 2. Phylum Cnidaria ................................................................................. 15 2.1. Class Anthozoa .................................................................................. 16 2.2. NRs in Cnidaria .................................................................................. 18 2.2.1. RXR in Cnidaria ................................................................................. 18 3. Objectives .......................................................................................... 19 Material and Methods ....................................................................................... 21 1. Biologic Material ................................................................................. 21 2. Genomic DNA Extraction ................................................................... 21 3. Total RNA Extraction .......................................................................... 22 4. Polymerase Chain Reaction (PCR) .................................................... 23 5. RT (Reverse Transcriptional) PCR ..................................................... 24 6. Rapid Amplification of cDNA Ends (RACE) ........................................ 25 7. TA cloning .......................................................................................... 26 8. Phylogenetic analysis ......................................................................... 26 Results ............................................................................................................. 27 1. Nucleic Acid extraction and comparison ............................................. 27 FCUP 5 Molecular analysis of Nuclear Receptors in the Class Anthozoa (Cnidaria) 2. FTZ-F1 and TR2/4 gene identification ................................................ 28 3. Partial NR gene isolation in A. sulcata ................................................ 30 4. Three genes amplification of NR2 family in A. sulcata ........................ 33 5. Phylogenetic relationships within NR2 family ..................................... 34 Discussion ........................................................................................................ 37 References ....................................................................................................... 42 Annexes ........................................................................................................... 46 FCUP 6 Molecular analysis of Nuclear Receptors in the Class Anthozoa (Cnidaria) LIST OF ABBREVIATIONS A - Absorbance AF-2 – Ligand Dependent Transactivation Function Domain 2 As_10 - Anemonia sulcata sequence similar to NvNR10 As_11 - Anemonia sulcata sequence similar to NvNR11 As_14 - Anemonia sulcata sequence similar to NvNR14 As_a – Anemonia sulcata RACE sequence BIC - Bayesian Information Criterion BLAST – Basic Local Alignment Search Tool C- Cytosine cDNA – complementary DeoxyriboNucleic Acid CDS – Coding Sequence COI - Cytochrome c-oxidase COUP-TF - Chicken Ovalbumin Upstream Promoter Transcription Factor CTAB - CetylTrimethylAmmonium Bromide
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