Functional elucidation of hypothetical proteins associated with lipid accumulation: Prioritizing genetic engineering targets for improved algal biofuel production

Abstract Growing attention on microalgae as potential biofuel feedstock has led to accumulation of several sequenced algal genomic data. Mining these genomes provides a huge opportunity to identify novel enzymes and pathways of biotechnological importance. However, the biggest challenge in the algal research is the association of function of the encoded protein sequences, which is primarily an automated process and includes only limited functional attributes with no detailed pathway, structure or genome-context annotation. Furthermore, in majority of the microalgae, nearly half of the proteome is still characterized as “hypothetical”, thereby impeding our understanding of the various metabolic processes and pathways. Recent studies have mentioned that genetic engineering approaches are important to improve lipid productivity for algal biofuel production, but the identities of majority of the enzymes involved remain unknown. In this study, the genomes of twenty-six microalgal species belonging to diverse phylogenetic lineages, including Cholorophyta, Rhodophyta, Heterokonta, Haptophyta, Cryptophyta and Dinoflagellate were examined to identify putative hypothetical proteins that might play a crucial role in lipid biosynthesis. Identification of homologous proteins in algae was inferred primarily by sequence similarity to experimentally known sequences of the plant Arabidopsis thaliana and subsequent filtering on the basis of conserved domains, gene ontology and analysis of metabolic pathway. Comprehensive sequence-structure annotation was predicted confidently for 285 putative hypothetical proteins with determination of active-site and 3D structural conformation of three vital enzymes. This is the first ever attempt to annotate hypothetical proteins across algal genomes that might be involved in lipid accumulation and thus promising targets for genetic engineering of oleaginous algal strains.