SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria

New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.

Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

Cyanobacteria are essential primary producers in marine ecosystems, playing an important role in both carbon and nitrogen cycles. In the last decade, various genome sequencing and metagenomic projects have generated large amounts of genetic data for cyanobacteria. This wealth of data provides researchers with a new basis for the study of molecular adaptation, ecology and evolution of cyanobacteria, as well as for developing biotechnological applications. It also facilitates the use of multiplex techniques, i.e., expression profiling by high-throughput technologies such as microarrays, RNA-seq, and proteomics. However, exploration and analysis of these data is challenging, and often requires advanced computational methods. Also, they need to be integrated into our existing framework of knowledge to use them to draw reliable biological conclusions. Here, systems biology provides important tools. Especially, the construction and analysis of molecular networks has emerged as a powerful systems-level framework, with which to integrate such data, and to better understand biological relevant processes in these organisms. In this review, we provide an overview of the advances and experimental approaches undertaken using multiplex data from genomic, transcriptomic, proteomic, and metabolomic studies in cyanobacteria. Furthermore, we summarize currently available web-based tools dedicated to cyanobacteria, i.e., CyanoBase, CyanoEXpress, ProPortal, Cyanorak, CyanoBIKE, and CINPER. Finally, we present a case study for the freshwater model cyanobacteria, Synechocystis sp. PCC6803, to show the power of meta-analysis, and the potential to extrapolate acquired knowledge to the ecologically important marine cyanobacteria genus, Prochlorococcus.

Highlights from the Indo-US workshop "Cyanobacteria: molecular networks to biofuels" held at Lonavala, India during December 16-20, 2012

An Indo-US workshop on "Cyanobacteria: molecular networks to biofuels" was held December 16-20, 2012 at Lagoona Resort, Lonavala, India. The workshop was jointly organized by two of the authors, PPW, a chemical engineer and LAS, a biologist, thereby ensuring a broad and cross-disciplinary participation. The main objective of the workshop was to bring researchers from academia and industry of the two countries together with common interests in cyanobacteria or microalgae and derived biofuels. An exchange of ideas resulted from a series of oral and poster presentations and, importantly, through one-on-one discussions during tea breaks and meals. Another key objective was to introduce young researchers of India to the exciting field of cyanobacterial physiology, modeling, and biofuels. PhD students and early stage researchers were especially encouraged to participate and about half of the 75 participants belonged to this category. The rest were comprised of senior researchers, including 13-15 invited speakers from each country. Overall, twenty-four institutes from 12 states of India were represented. The deliberations, which are being compiled in the present special issue, revolved mainly around molecular aspects of cyanobacterial biofuels including metabolic engineering, networks, genetic regulation, circadian rhythms, and stress responses. Representatives of some key funding agencies and industry provided a perspective and opportunities in the field and for bilateral collaboration. This article summarizes deliberations that took place at the meeting and provides a bird's eye view of the ongoing research in the field in the two countries.