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Gene. 2013 Oct 10;528(2):109-19. doi: 10.1016/j.gene.2013.07.039. Epub 2013 Jul 28.

Unraveling microalgal molecular interactions using evolutionary and structural bioinformatics.

Author information

1
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:

3D; 6,7-dimethyl-8-(1′-d-ribityl)-lumanizine; 6-phosphogluconate dehydrogenase; 6PGDH; ATP; Adenosine triphosphate; BLAST; Basic Local Alignment Search Tool; CO(2); COX2A; COX2B; Carbon dioxide; DHAP; DMRL; DOT1; Disruptor of Telomeric silencing; Fra10Ac1; Fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1; G3P; G6PDH; GAPDH; Gene fission; Gene fusion; Homology modeling; MEP; MOE; Microalgae; Molecular Operating Environment; Molecular electrostatic potential; NCBI; NPS; NVT; National Center for Biotechnology Information; Network Protein Sequence Analysis; Number of atoms, Volume and Temperature; PDB; Protein Data Bank; Protein association; RMSD; RNA; Ribonucleic acid; Root-mean-square deviation; SAFE; SH3; Software for the Analysis of Fusion Events; Src homology 3 domain; TIM; Three-dimensional; Triosephosphate isomerase; Trp-Asp; WD; cytochrome c oxidase subunit II C-terminal; cytochrome c oxidase subunit II, transmembrane domain; d-Glyceraldehyde 3-phosphate; dihydroxyacetone phosphate; glucose-6-phosphate 1-dehydrogenase; glyceraldehyde-3-phosphate dehydrogenase

PMID:
23900196
DOI:
10.1016/j.gene.2013.07.039
[Indexed for MEDLINE]

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