Biology subjects

Koziej, L.

Publications and source records attributed to Koziej, L..

3 recordsLinked to original sources

bioRxiv2025

Encapsidic production and isolation of degradation-prone polypeptides

Degradation during production and delivery is a significant bottleneck in developing biomolecular therapies. Here, we show that encapsulation in protein cages formed by engineered variants of a cage-forming lumazine synthase establishes an effective route for microbial production and isolation of otherwise difficult-to-express, degradation-prone polypeptides. In this system, genetic fusion to a cage component protomer ensures efficient guest packaging while being produced in host bacterial cells. Meanwhile, the controlled opening outside the cellular context allows facile isolation of cargo via sequence-specific protease cleavage. Furthermore, modular patchwork assembly avoids guest overloading, preventing unwanted incomplete cage assembly and the formation of insoluble aggregates. The general applicability of our "encapsidic" production approach was demonstrated by the efficient production of six intrinsically disordered polypeptides that have proven therapeutic potentials.

bioengineering↗

bioRxiv2024

Dynamic assembly of pentamer-based protein nanotubes

The molecular mechanisms and the geometrical theory underlying the polymorphic behavior of protein cages provide a basis for designing ones with the desired morphology and assembly properties. We show here that a circularly permuted cage-forming enzyme can controllably assemble into a variety of hollow spherical and cylindrical structures composed entirely of pentamers. A dramatic cage-to-tube transformation is facilitated by an untethered -helix domain that prevents the 3-fold symmetry interaction and imparts a torsion between the building blocks. The unique double- and triple-stranded helical arrangements of subunits are mathematically optimal tiling patterns for this type of pentamer. These structural insights afford guidelines for the design of customized protein nanotubes for smart delivery and nanoreactor systems.

bioengineering↗

bioRxiv2024

Codon Pair-Specific Translation Defects Trigger Ribosome-Associated Quality Control to Avoid Proteotoxic Stress

tRNA modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding, but how codon optimality defects trigger cellular phenotypes remains unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs, triggering ribosome collisions and inducing a coordinated and hierarchical response of cellular quality control pathways. Ribosome profiling reveals an unexpected functional diversity for wobble-uridine (U34) modifications during decoding. The same modification can have different effects at the A and P sites. Furthermore, modification-dependent stalling codon pairs induce ribosome collisions, triggering ribosome-associated quality control (RQC) to prevent protein aggregation by degrading aberrant nascent peptides and mRNAs. RQC inactivation stimulates the expression of molecular chaperones to remove protein aggregates. Our results show that loss of tRNA modifications primarily disrupts translation rates of suboptimal codon pairs and reveal the coordinated regulation and adaptability of cellular surveillance systems to ensure efficient and accurate protein synthesis and maintain protein homeostasis.

biochemistry↗