Zilberzwige Tal Lab

Architectures of Bacterial Immunity

Research

Intelligent regulatory networks are at the core of bacterial survival, enabling cells to sense, compute, and adapt to fluctuating environments with remarkable precision. A central feature of these networks is the intricate interplay between RNA and proteins, which together form a sophisticated regulatory language that our lab is beginning to decipher.

Our research is dedicated to decoding this language by focusing on key RNA-protein systems in bacteria that control cellular fate, including those that can trigger programmed cell death, such as toxin-antitoxin modules. We seek to uncover the evolutionary logic and molecular mechanisms that have sculpted these powerful systems.

By combining experimental and computational approaches including molecular genetics, biochemistry, bioinformatics, and single-cell analysis we reveal how bacteria compute with RNA and proteins, and how these principles can be repurposed to engineer programmable biological intelligence.

Research page

The Language of RNA and Proteins

From Single Cells to Communities

Re-Engineering Nature

Selected Publications

Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

Zilberzwige-Tal S., Altae-Tran H., Kannan S., Wilkinson M. E., Vo S. C. D. T., Strebinger D., Edmonds K. H. K., Yao C. C. J., Mears K. S., Shmakov S. A., Makarova K. S., Macrae R. K., Koonin E. V. & Zhang F. (2025) Cell. 188, 7, p. 1925-1940.e20

Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood. Here, we describe an integrated sequence/structure evolutionary tracing approach to identify the ancestors of the RNA-targeting CRISPR-Cas13 system. We find that Cas13 likely evolved from AbiF, which is encoded by an abortive infection-linked gene that is stably associated with a conserved non-coding RNA (ncRNA). We further characterize a miniature Cas13, classified here as Cas13e, which serves as an evolutionary intermediate between AbiF and other known Cas13s. Despite this relationship, we show that their functions substantially differ. Whereas Cas13e is an RNA-guided RNA-targeting system, AbiF is a toxin-antitoxin (TA) system with an RNA antitoxin. We solve the structure of AbiF using cryoelectron microscopy (cryo-EM), revealing basic structural alterations that set Cas13s apart from AbiF. Finally, we map the key structural changes that enabled a non-guided TA system to evolve into an RNA-guided CRISPR system.

Hierarchically porous carnosine-Zn microspheres

Chen Y., Zilberzwige-Tal S., Rosenmann N. D., Oktawiec J., Nensel A. K., Ma Q., Lichtenstein S., Gazit E. & Gianneschi N. C. (2025) Matter. 8, 9, 102108.

Hierarchically porous materials have broad applications in biotechnology and medicine, yet current fabrication methods often lack scalability and biocompatibility. Here, we present a peptide-coordination self-assembly approach to prepare hierarchically porous microspheres composed of naturally occurring carnosine dipeptide and coordinated Zn(II) ions. Metal coordination led to microsphere formation featuring interconnected channels with a hierarchically porous structure. Characterization with scanning electron and transmission electron microscopy, as well as with extended X-ray absorption fine structure, confirmed its nanofibrous architecture and local Zn(II) coordination environment. Liquid cell transmission electron microscopy, in turn, provided real-time insight into the assembly process, revealing a stepwise process from nanoclusters to nanofibers and ultimately to porous microspheres. The carnosine-Zn(II) microspheres exhibit intrinsic blue fluorescence and high porosity, containing both micropores and mesopores, which facilitate efficient mass transport and biomolecule immobilization. We leverage these properties to generate reusable, cell-free synthesis nanoreactors, to enhance DNA transcription and translation and protect against nuclease degradation.

On-Chip De Novo Production of mRNA Vaccine in Lipid Nanoparticles

Zilberzwige-Tal S., Levin A., Ezra A., Elia U., Finkelstein-Zuta G., Kreiser T., Gershon L., Goldsmith M., Kon E., Navon Y., Cohen O., Knowles T. P., Peer D. & Gazit E. (2025) Small. 21, 32, 2500114.

RNA-based therapeutics have revolutionized precision medicine due to their unprecedented potency, specificity, and adaptability. However, the inherent limited stability of RNA, including mRNA used in vaccines, is a major obstacle to the full realization of their potential. This instability, coupled with the centralized nature of vaccine production, currently limits the generation of RNA therapeutics at the point of care, which will otherwise fully harness the potential of these agents. Here, a microfluidic platform is presented for on-demand, personalized synthesis of modified mRNA stabilized by lipid nanoparticles. The design includes trapped biotinylated DNA, tagged T7 RNA polymerase, and a Tesla mixer, allowing the on-chip synthesis, purification, and encapsulation of mRNA in uniform lipid nanoparticles (LNPs), all conducted seamlessly on the same microfluidic device. This on-chip microfluidic synthesis approach is found to match standardized mRNA production yields, yet surpasses typical purification methods. Furthermore, as a proof-of-concept, the versatility and efficacy of the platform are demonstrated by generating diverse RNA sequences and structures, exhibiting functionality in human cell lines and mouse models. Moreover, an active SARS-CoV-2 vaccine is successfully engineered, highlighting the platform's potential for personalized vaccination strategies and offering a promising avenue for high throughput, decentralized vaccine delivery, reduced cold chain dependence, and even advancing current personalized medicine approaches through custom RNA therapeutics.

All Publications