RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR

Concentration-Dependent CsrA Regulation of the uxuB Transcript Leads to Development of a Post-Transcriptional Bandpass Filter

Post-transcriptional control systems offer new avenues for designing synthetic circuits that provide reduced burden and fewer synthetic regulatory components compared to transcriptionally based tools. Herein, we repurpose a newly identified post-transcriptional interaction between the uxuB mRNA transcript, specifically the 5' UTR + 100 nucleotides of coding sequence (100 nt CDS), and the E. coli Carbon Storage Regulatory A (CsrA) protein to design a biological post-transcriptional bandpass filter. In this work, we characterize the uxuB mRNA as a heterogeneous target of CsrA, where the protein can both activate and repress uxuB activity depending on its intracellular concentration. We leverage this interaction to implement a novel strategy of regulation within the 5' UTR of an mRNA. Specifically, we report a hierarchical binding strategy that may be leveraged by CsrA within uxuB to produce a dose-dependent response in regulatory outcomes. In our semisynthetic circuit, the uxuB 5' UTR + 100 nt CDS sequence is used as a scaffold that is fused to a gene of interest, which allows the circuit to transition between ON/OFF states based on the concentration range of free natively expressed CsrA. Notably, this system exerts regulation comparable to previously developed transcriptional bandpass filters while reducing the number of synthetic circuit components and can be used in concert with additional post-transcriptionally controlled circuits to achieve complex multi-signal control. We anticipate that future characterization of native regulatory RNA-protein systems will enable the development of more complex RNP-based circuits for synthetic biology applications.

Liquid-liquid phase separation in diseases

Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.

RNAs as Sensors of Oxidative Stress in Bacteria

Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.