Applications of phage-derived RNA-based technologies in synthetic biology

Abstract

As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.

Advance on Engineering of Bacteriophages by Synthetic Biology

“…With the quick spread of AMR and the slow pace of new antibiotics discovery, the design and development of phage or phage functional elements, as novel and alternative antibacterial therapies, detection and diagnostic tools, have been proposed and implemented (Figure 4). [127][128][129] As well, developing a more convenient phage display technique is needed for protein engineering. In this new journey, the road ahead is still long.…”

Design of artificial small regulatory trans-RNA for gene knockdown in Bacillus subtilis

“…This sRNA system with cross-species activity not only enriched the gene regulation toolkit in synthetic biology for B. subtilis and E. coli but also enhanced our understanding of trans -acting sRNAs. In addition, by coupling with the advances in promoter engineering [ 34 ], protein-based regulators [ 52 ], CRISPR/Cas systems [ 53 ], RNA-based regulators [ 54 , 55 ], increasingly sophisticated forms of gene circuits for highly programmable and dynamic biological functions should be constructed in near future.…”

Rekindling of a Masterful Precedent; Bacteriophage: Reappraisal and Future Pursuits

“…However, this will require further elucidation of their protein structures and host interactions. Luckily, the cryo-EM has precipitated a breakthrough; it was possible for the first time to closely examine the ssRNA phage and view its genome within the capsid, revealing their 3D-structure ( van Duin, 1988 ; Poranen et al., 2005 ; Uzan, 2009 ; Callanan et al., 2018 ; Zhang and Wu, 2020 ).…”