De novo non-compartmentalized microorganism for directed evolution of nanobodies

The creation of de novo microorganisms is a fascinating task, and microorganisms offer a wide range of applications for humanity. Herein, we designed a de novo microorganism, termed Syn-phage, as an artificial unencapsulated mimic of naturally occurring phage capable of evolving nanobodies with improved properties. Syn-phage composes unified genomic and phenotypic materials with phenotypic proteins encoded from its genetic information. Since Syn-phage can undergo amplification in E. coli. host, we established a protocol for the evolution of nanobodies with improved avidity or affinity, allowing super-resolution live-cell immunoimaging of endogenous proteins, a challenge posed in immunolabeling with antibodies. Utilizing a Syn-phage evolved nanobody, we visualized the microtubule nucleation factor hTPX2, recorded the dynamics of it during mitotic progression, and imaged it at a resolution beyond the diffraction limit of light via an AI-powered imaging pipeline. Hence, this study demonstrated the possibility to design de novo microorganisms for capitative applications.