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An Investigation of Sunlight Stress Response Genes in the Intertidal Sea Anemone, Actinia Tenebrosa

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An Investigation of Sunlight Stress Response Genes in the Intertidal Sea Anemone, Actinia Tenebrosa AN INVESTIGATION OF SUNLIGHT STRESS RESPONSE GENES IN THE INTERTIDAL SEA ANEMONE, ACTINIA TENEBROSA Jonathon Noel Muller Bachelor of Applied Science, Environmental Science (Honours) Submitted in fulfilment of the requirements for the degree of Master of Applied Science (Research) School of Earth, Environment and Biological Sciences Science and Engineering Faculty Queensland University of Technology 2016 Keywords Actinia tenebrosa, actiniarian, antioxidant, cellular stress response, cnidarian, DNA repair, intertidal, sunlight, UV, UV screening, sea anemone Images and photographs All photographs, diagrams, illustrations and other images in this thesis are the intellectual property of the author Jonathon Muller 2016, unless explicitly stated. Abstract Organisms living in the intertidal zone are subjected to the impacts of climate change, and understanding their response to environmental conditions is becoming increasingly important. Direct exposure to sunlight can be hazardous to many organisms that inhabit the intertidal zone, and it is likely to interact synergistically with desiccation stress. Some intertidal sea anemone species (Phylum Cnidaria) withstand periodic sunlight exposure at low tide, yet lack the physical barriers and/or stratified epithelium that allow other sedentary intertidal organisms to survive in this environment. Sea anemones that inhabit intertidal areas may possess unique adaptations to withstand significant sunlight exposure, and the genetic basis of their stress response needs to be investigated. Sea anemones are important components of rocky intertidal ecosystems along Australian coastlines, yet virtually nothing is known about their response to sunlight stress or susceptibility to changing environmental conditions. The Waratah anemone, Actinia tenebrosa, is an excellent indicator species for understanding stress tolerances in intertidal sea anemones and may provide important insights into how other species will respond to a changing environment. In chapter two, the sequenced (~7 Gbp) transcriptome of the sea anemone, Actinia tenebrosa, was assembled and annotated, and genes involved in the UV response identified. From this data set, full-length sunlight stress response genes were identified and compared across existing sequenced cnidarian genomes. Comparative and phylogenetic analysis of candidate UV stress response genes (i.e. blue chromoprotein, CPD photolyase and RAD23b) and one novel bioluminescent gene (photoprotein) were conducted across the cnidarians. Eight hundred and sixty two UV response genes were identified in A. tenebrosa and 179 were determined to have full length open reading frames. These 179 full length genes were found to be widely distributed across cnidarian species. This represents the first detailed investigation of the bioluminescent-associated photoprotein gene family in cnidarians. Both chromoprotein and photoprotein occurred as gene families in cnidarians, while CPD photolyase and UV excision repair RAD23 were present as single copy genes. In chapter three, a detailed investigation of four candidate sunlight stress genes from A. tenebrosa was conducted, specifically, blue chromoprotein (UV and visible light screening/non-enzymatic antioxidant), CPD photolyase (DNA repair), and Cu- Zn SOD and Fe/Mn SOD (enzymatic antioxidants) at the northern limit of its distribution, where temperature and UV are at their highest. Actinia tenebrosa individuals were subjected to four sunlight stress treatments (submerged dark, submerged light, exposed dark and exposed light) and qPCR was used to determine patterns of sunlight stress induced gene expression in the four candidate genes. Comparative and phylogenetic analysis of these candidate UV stress response genes was then conducted across the sea anemones. CPD photolyase and Fe/Mn SOD expression significantly increased over time when submerged under sunlight, but not when exposed under sunlight, and that UV and photosynthetically active radiation (PAR) were the best environmental predictors for the increase. It may be concluded that desiccation stress may invoke a different response, and that the up-regulation of CPD photolyase and Fe/Mn SOD, and perhaps other sunlight stress response genes, may not be as important when the organism is aerially exposed. In addition, the first detailed comparison of the candidate gene families in sea anemones was conducted and two new full-length Fe/Mn SODs gene families identified. This thesis has provided many usefuls insights into the genes involved in A. tenebrosas sunlight stress resilience and provides a resource to better understand the molecular mechanisms that enable A. tenebrosa to survive periodic UV stress. The investigation of candidate stress genes in A. tenebrosa provides a first look at how an intertidal sea anemone tolerates sunlight stress, which can be used to better understand how other intertidal sea anemone species will respond to changing climactic conditions. Table of Contents Keywords ................................................................................................................................. 2 Table of Contents ..................................................................................................................... 6 List of Figures .......................................................................................................................... 8 List of Tables .......................................................................................................................... 10 Statement of Original Authorship .......................................................................................... 11 Acknowledgements ................................................................................................................ 12 Chapter 1: Literature review .................................................................................... 1 Overview .................................................................................................................................. 2 Introduction .............................................................................................................................. 2 Sunlight stress .......................................................................................................................... 2 UV and visible light screening ................................................................................................. 6 DNA damage repair................................................................................................................ 10 Direct DNA damage repair .......................................................................................... 10 Indirect DNA damage repair ........................................................................................ 13 Antioxidants ........................................................................................................................... 14 Enzymatic antioxidants ................................................................................................ 14 Non-enzymatic antioxidants......................................................................................... 15 Molecular chaperones ............................................................................................................. 17 Conclusions ............................................................................................................................ 19 Project aims ............................................................................................................................ 22 Chapter 2: Comparative analysis of genes involved in UV response from cnidarian species ....................................................................................................... 25 Abstract .................................................................................................................................. 26 Introduction ............................................................................................................................ 27 Materials and methods............................................................................................................ 30 Sample collection, RNA extraction and sequencing .................................................... 30 Data processing and assembly ..................................................................................... 31 Comparative and phylogenetic analysis ....................................................................... 31 Results .................................................................................................................................... 34 Sequencing, data processing and assembly .................................................................. 34 Comparative and phylogenetic analysis of candidate genes ........................................ 34 Discussion .............................................................................................................................. 43 Conclusions ............................................................................................................................ 50 Chapter 3: Gene expression changes in response to sunlight stress in the intertidal cnidarian, Actinia tenebrosa ................................................................... 53 Abstract .................................................................................................................................. 54 Introduction ...........................................................................................................................
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