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Unraveling microalgal molecular interactions using evolutionary and structural bioinformatics
Authors:Dimitrios Vlachakis  Athanasia PavlopoulouDorothea Kazazi  Sophia Kossida
Institution:Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
Abstract:Microalgae are unicellular microorganisms indispensible for environmental stability and life on earth, because they produce approximately half of the atmospheric oxygen, with simultaneously feeding on the harmful greenhouse gas carbon dioxide. Using gene fusion analysis, a series of five fusion/fission events was identified, that provided the basis for critical insights to their evolutionary history. Moreover, the three-dimensional structures of both the fused and the component proteins were predicted, allowing us to envisage putative protein–protein interactions that are invaluable for the efficient usage, handling and exploitation of microalgae. Collectively, our proposed approach on the five fusion/fission alga protein events contributes towards the expansion of the microalgae knowledgebase, bridging protein evolution of the ancient microalgal species and the rapidly evolving, modern, bioinformatics field.
Keywords:CO2  Carbon dioxide  SAFE  Software for the Analysis of Fusion Events  3D  Three-dimensional  BLAST  Basic Local Alignment Search Tool  Fra10Ac1  Fragile site  folic acid type  rare  fra(10)(q23  3) or fra(10)(q24  2) candidate 1  DOT1  Disruptor of Telomeric silencing  COX2A  cytochrome c oxidase subunit II  transmembrane domain  COX2B  cytochrome c oxidase subunit II C-terminal  G6PDH  glucose-6-phosphate 1-dehydrogenase  TIM  Triosephosphate isomerase  6PGDH  6-phosphogluconate dehydrogenase  GAPDH  glyceraldehyde-3-phosphate dehydrogenase  DMRL  6  7-dimethyl-8-(1&prime  -d-ribityl)-lumanizine  G3P  d-Glyceraldehyde 3-phosphate  DHAP  dihydroxyacetone phosphate  PDB  Protein Data Bank  RNA  Ribonucleic acid  NCBI  National Center for Biotechnology Information  ATP  Adenosine triphosphate  WD  Trp-Asp  SH3  Src homology 3 domain  NPS  Network Protein Sequence Analysis  MOE  Molecular Operating Environment  MEP  Molecular electrostatic potential  NVT  Number of atoms  Volume and Temperature  RMSD  Root-mean-square deviation
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