Zilberzwige Tal Lab

Architectures of Bacterial Immunity

Research

We believe that understanding how living cells sense, adapt, and make decisions is one of biology’s greatest challenges.

Every living cell continuously interprets its surroundings, integrates countless molecular signals, and responds with remarkable precision. These decisions determine whether a cell grows, survives, adapts, or dies.

We believe that uncovering the molecular principles behind these processes is essential for understanding life itself. Beyond revealing fundamental biology, these discoveries provide the foundation for designing new biological systems that can address challenges in medicine, biotechnology, and beyond.

We decode the molecular language that enables cellular decision-making.

Our research combines molecular genetics, biochemistry, synthetic biology, bioinformatics, and single-cell approaches to uncover how regulatory networks operate at the molecular level.

We focus on the intricate interplay between RNA and proteins-dynamic interactions that allow cells to sense environmental changes, coordinate complex responses, and determine cellular fate. By studying these systems across multiple scales, from molecular mechanisms to evolutionary history, we seek to reveal the principles that govern cellular behavior.

We study bacterial RNA-protein systems.

Our laboratory investigates bacterial regulatory networks, with a particular focus on RNA-protein interactions that control stress responses, adaptation, and programmed cell death, including toxin-antitoxin systems.

By uncovering how these regulatory systems function and evolve, we aim not only to deepen our understanding of bacterial biology but also to inspire new approaches for engineering programmable biological systems.

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