A Direct RNA-to-RNA Replication System for Enhanced Gene Expression in Bacteria

Design of Novel Synthetic RNA Replicons Based on Emesvirus zinderi

Self-replicating RNAs (srRNAs) are synthetic molecules designed to mimic the self-replicating ability of viral RNAs. srRNAs hold significant promise for a range of applications, including enhancing protein expression, reprogramming cells into pluripotent stem cells, and creating cell-free systems for experimental evolution. However, the development of srRNAs for use in bacterial systems remains limited. Here, we demonstrate how a srRNA scaffold from Emesvirus zinderi can be engineered into a self-encoding srRNA by incorporating the coding region of the catalytically active replicase subunit. With the help of in vitro replication assays, including an in vitro translation-coupled replication approach, we show that the resulting system enables complete replication cycles of RNA both in cis and trans, including long cargo RNAs such as tethered 5S, 16S, and 23S rRNAs. In summary, our findings suggest that these srRNAs have significant potential for fundamental research, synthetic biology, and general in vitro evolution.

Design principles and applications of synthetic self-replicating RNAs

With the advent of ever more sophisticated methods for the in vitro synthesis and the in vivo delivery of RNAs, synthetic mRNAs have gained substantial interest both for medical applications, as well as for biotechnology. However, in most biological systems exogeneous mRNAs possess only a limited half-life, especially in fast dividing cells. In contrast, viral RNAs can extend their lifetime by actively replicating inside their host. As such they may serve as scaffolds for the design of synthetic self-replicating RNAs (srRNA), which can be used to increase both the half-life and intracellular concentration of coding RNAs. Synthetic srRNAs may be used to enhance recombinant protein expression or induce the reprogramming of differentiated cells into pluripotent stem cells but also to create cell-free systems for research based on experimental evolution. In this article, we discuss the applications and design principles of srRNAs used for cellular reprogramming, mRNA-based vaccines and tools for synthetic biology. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.

In vitro characterisation of the MS2 RNA polymerase complex reveals host factors that modulate emesviral replicase activity

The RNA phage MS2 is one of the most important model organisms in molecular biology and virology. Despite its comprehensive characterisation, the composition of the RNA replication machinery remained obscure. Here, we characterised host proteins required to reconstitute the functional replicase in vitro. By combining a purified replicase sub-complex with elements of an in vitro translation system, we confirmed that the three host factors, EF-Ts, EF-Tu, and ribosomal protein S1, are part of the active replicase holocomplex. Furthermore, we found that the translation initiation factors IF1 and IF3 modulate replicase activity. While IF3 directly competes with the replicase for template binding, IF1 appears to act as an RNA chaperone that facilitates polymerase readthrough. Finally, we demonstrate in vitro formation of RNAs containing minimal motifs required for amplification. Our work sheds light on the MS2 replication machinery and provides a new promising platform for cell-free evolution.

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

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.