Green genes: bioinformatics and systems-biology innovations drive algal biotechnology

Abstract

Many species of microalgae produce hydrocarbons, polysaccharides, and other valuable products in significant amounts. However, large-scale production of algal products is not yet competitive against non-renewable alternatives from fossil fuel. Metabolic engineering approaches will help to improve productivity, but the exact metabolic pathways and the identities of the majority of the genes involved remain unknown. Recent advances in bioinformatics and systems-biology modeling coupled with increasing numbers of algal genome-sequencing projects are providing the means to address this. A multidisciplinary integration of methods will provide synergy for a systems-level understanding of microalgae, and thereby accelerate the improvement of industrially valuable strains. In this review we highlight recent advances and challenges to microalgal research and discuss future potential.

Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis

“…Mathematical and kinetic models have also been developed to study growth parameters and lipid production in green algae (Packer et al, 2010, Tevatia et al, 2012, Yang et al, 2010. Taken together, current developments in molecular genetics and biochemistry, omics (including genomics, transcriptomics, proteomics, metabolomics, and fluxomics, integrative modeling, and genome engineering tools have the potential to enable precise predictive capabilities and rational engineering of algae for high lipid content, see Figure 1 (Jiang et al, 2014, Recht et al, 2014, Reijnders et al, 2014. The above technological advances offer a unique opportunity to understand algal lipid metabolism in a holistic manner.…”

“…The other article describes the ways in which the models represent parts of the metabolism, such as photosynthesis, as well as how biomass and macromolecules are represented (Baroukh et al, 2015b). Another review written by Reijnders et al briefly covers the different models in existence as of 2014 but does not go into detail about them individually, with only brief discussion of the types of models (Reijnders et al, 2014). A review by De Bhowmick et al discussed methods of metabolic engineering using techniques such as FBA, but did not provide details of how the individual models work (De Bhowmick et al, 2015).…”

An overview on biofuel and biochemical production by photosynthetic microorganisms with understanding of the metabolism and by metabolic engineering together with efficient cultivation and downstream processing

“…The systems biology approach plays a crucial role for function prediction based on the database with proper metabolic modeling [109].…”

Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes

“…However, while several studies in the biofuel sector have investigated selection, cultivation, extraction and purification of specific algal species and strains (Carvalho et al 2006, Chisti 2007), a consensus has not yet been reached on costs and best practices in algal production (Passell et al 2013, Medipally et al 2015). Thus, studies investigating the development of practical and effective algal production techniques are important, and will improve our understanding of both aquatic and terrestrial plants, considering that algae are common ancestors of vascular plants (Reijnders et al 2014, Bhattacharya et al 2015). …”

“…Subsequently, next-generation applications, including sequence assembly tools and gene prediction tools, have enabled the sequencing of algal species (Kim et al 2014). As a result, over 30 whole algal genomes have been sequenced to date (Kim et al 2014, Reijnders et al 2014). These representative genomes, except for those of the two species mentioned above, include the green algae Ostreococcus tauri (Derelle et al 2006) and Chlamydomonas reinhardtii (Merchant et al 2007) of the Viridiplantae kingdom (including green plants), the red alga Galdieria sulphuraria (Schonknecht et al 2013) and the glaucophyte Cyanophora paradoxa (Price et al 2012).…”