Microorganisms have been exploited as cell factories, an alternative for petrochemical industries constrained by limited resources and energies. Their ability to utilize multiple carbon sources, from C1 gas to complex biomass, has a potential for cost-effective, sustainable energy generation 1, 2, 3, 4. Engineered microbes can also produce various natural- or non-natural biomolecules such as biofuels, platform chemicals, food additives, and valuable medicine 5, 6, suggesting their versatility. However, wild-type strains are generally not optimized for metabolic fermentation and should be engineered to enhance production yield.

Various biological tools and strategies have been used to introduce heterologous metabolic pathways into the microbial hosts and regulate their gene expression and physiology. Not more than 10 years ago, the construction of complex genetic circuits or high-throughput tests was still challenging, causing the limit of microbial engineering and its applicability 7, 8. Recently developed devices have shown exquisiteness and programmability, expanding the boundaries of controllable physiology. For example, those devices can simultaneously control multiple genes 9, 10, 11 and modify specific strains in the microbial consortium 12••, 13•. Besides, they can dynamically control metabolic flux or cell growth, depending on target biomolecules or environmental signals 14, 15, 16, 17.

Among the various programmable synthetic biology tools, three categories showed noticeable advancement and expanded their universality: biosensors, clustered regularly interspaced short palindromic repeats with Cas proteins (CRISPR–Cas), and RNA devices. Since these tools have modularity and orthogonality, they can be easily applied to diverse hosts and multiple conditions. They control gene replication, transcription, and translation level, and are often combined for synergistic and complex output. This review focuses on the characteristics and achievements of these programmable tools concerning applicability to energy biotechnology (Table 1).