Genes implicated in the storage and the production of energy : bioinformatics approach and application in coral reefs in Singapore.
Seow, Wan Yi.
Date of Issue2012
School of Biological Sciences
Nanyang Environment and Water Research Institute
Coral reefs are important ecosystems of the ocean. However anthropogenic disturbances threaten their survival. Corals are associated with photosynthetic zooxanthellae from the genus Symbiodinium and coral hosts obtain up to 90% of its energy resources from the symbiont. However, little attention has been paid to studying the transciptomics of corals and their symbionts simultaneously. A bioinformatics approach was used to study ATP synthase subunit beta and malonyl-CoA-acyl carrier protein transacylase (MCAT), genes implicated in the storage and production of energy. 55 MCAT and 77 ATP synthase subunit beta protein and nucleotide sequences from marine clades were retrieved from the NCBI database using BLAST. Sequences were aligned using ClustalW2 and primers specific to corals and zooxanthellae were designed. Protein 3D structures were predicted using SWISS-MODEL and structure conservation was investigated. Both proteins have largely conserved 3D structures, although the protein sequence of MCAT was much less conserved (47% average identity compared to Homo sapiens MCAT) compared to that in ATP synthase subunit beta (83% average identity compared to bovine ATP synthase subunit beta). Coral samples were collected from Pulau Hantu and DNA and RNA extractions were carried out. Preliminary testing has shown that zooxanthellae RNA extractions were successful from coral samples.
Final Year Project (FYP)
Nanyang Technological University