Cell-free expression of RNA encoded genes using MS2 replicase

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.

Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes through experimental evolution

The integration of individually replicating genes into a primitive chromosome is a key evolutionary transition in the development of life, allowing the simultaneous inheritance of genes. However, how this transition occurred is unclear because the extended size of primitive chromosomes replicate slower than unlinked genes. Theoretical studies have suggested that a primitive chromosome can evolve in the presence of cell-like compartments, as the physical linkage prevents the stochastic loss of essential genes upon division, but experimental support for this is lacking. Here, we demonstrate the evolution of a chromosome-like RNA from two cooperative RNA replicators encoding replication and metabolic enzymes. Through their long-term replication in cell-like compartments, linked RNAs emerged with the two cooperative RNAs connected end-to-end. The linked RNAs had different mutation patterns than the two unlinked RNAs, suggesting that they were maintained as partially distinct lineages in the population. Our results provide experimental evidence supporting the plausibility of the evolution of a primitive chromosome from unlinked gene fragments, an important step in the emergence of complex biological systems.

Programmable Synthesis of Biobased Materials Using Cell-Free Systems

Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.

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.

Clinical and experimental bacteriophage studies: Recommendations for possible approaches for standing against SARS-CoV-2

In 2019, the world faced a serious health challenge, the rapid spreading of a life-threatening viral pneumonia, coronavirus disease 2019 (COVID-19) caused by a betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of January 2022 WHO statistics shows more than 5.6 million death and about 350 million infection by SARS-CoV-2. One of the life threatening aspects of COVID-19 is secondary infections and reduced efficacy of antibiotics against them. Since the beginning of COVID-19 many researches have been done on identification, treatment, and vaccine development. Bacterial viruses (bacteriophages) could offer novel approaches to detect, treat and control COVID-19. Phage therapy and in particular using phage cocktails can be used to control or eliminate the bacterial pathogen as an alternative or complementary therapeutic agent. At the same time, phage interaction with the host immune system can regulate the inflammatory response. In addition, phage display and engineered synthetic phages can be utilized to develop new vaccines and antibodies, stimulate the immune system, and elicit a rapid and well-appropriate defense response. The emergence of SARS-CoV-2 new variants like delta and omicron has proved the urgent need for precise, efficient and novel approaches for vaccine development and virus detection techniques in which bacteriophages may be one of the plausible solutions. Therefore, phages with similar morphology and/or genetic content to that of coronaviruses can be used for ecological and epidemiological modeling of SARS-CoV-2 behavior and future generations of coronavirus, and in general new viral pathogens. This article is a comprehensive review/perspective of potential applications of bacteriophages in the fight against the present pandemic and the post-COVID era.

Optimising protein synthesis in cell‐free systems, a review

Over the last decades, cell-free systems have been extensively used for in vitro protein expression. A vast range of protocols and cellular sources varying from prokaryotes and eukaryotes are now available for cell-free technology. However, exploiting the maximum capacity of cell free systems is not achieved by using traditional protocols. Here, what are the strategies and choices one can apply to optimise cell-free protein synthesis have been reviewed. These strategies provide robust and informative improvements regarding transcription, translation and protein folding which can later be used for the establishment of individual best cell-free reactions per lysate batch.

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.