Biology subjects

Iburg, M.

Publications and source records attributed to Iburg, M..

3 recordsLinked to original sources

bioRxiv2026

Transcriptomic and proteomic responses to gas vesicle collapse in native and engineered bacterial systems

Gas vesicles (GVs) are air-filled protein nanostructures produced by microbes to regulate buoyancy and have emerged as powerful tools in biomedical imaging, particularly as acoustic reporter genes. Their mechanically robust shells enclose a stable air compartment, which collapses irreversibly when subjected to sufficient hydrostatic or acoustic pressure, leaving behind large protein sheets. This collapse phenomenon underlies key applications such as differential imaging and controlled cavitation and is also believed to occur naturally during buoyancy regulation, yet its physiological consequences remain poorly understood. Here, we used transcriptomic and proteomic approaches to investigate cellular responses to GV collapse. In the native GV-producing cyanobacterium Dolichospermum flos-aquae, RNA sequencing revealed a distinct transcriptional response characterized by the upregulation of heat shock proteins, indicative of a stress reaction to intracellular protein aggregation. In contrast, bioluminescence reporter assays in E. coli heterologously expressing GVs showed no comparable activation of heat shock promoters. To test the hypothesis that collapsed GVs can be recognized by specific proteins inside cells, we conducted LC-MS/MS-based pull-down assays in both species but did not identify strong candidate binders. While no definitive recognition mechanism was uncovered, our omics-based study provides a rich dataset for cellular responses to GV collapse in both the native and heterologous systems. These findings suggest that cellular responses to collapsed GVs may be more complex than previously recognized, and that both improved assay sensitivity and additional focused experiments will be needed to elucidate how cells detect and manage large intracellular protein aggregates such as collapsed gas vesicles. Proteomics data are available via ProteomeXchange (PXD060779), and RNA sequencing data via NCBI GEO (GSE289028).

synthetic biology↗

bioRxiv2023

Elucidating the assembly of gas vesicles by systematic protein-protein interaction analysis

Gas vesicles (GVs) are gas-filled microbial organelles formed by unique 3-nm thick, amphipathic, force-bearing protein shells, which can withstand multiple atmospheric pressures and maintain a physically stable air bubble with megapascal surface tension. However, the molecular process to assemble this shell remains elusive: while 6-8 assembly factor proteins were identified as essential, none of them have a defined function. As one of the first steps to elucidate the assembly mechanism, we devise a high-throughput in vivo assay to determine the interactions of all 11 proteins in a GV operon. Complete or partial deletions of the operon establish the interdependence relationship of the interaction on the background GV proteins with additional information on assembly tolerance and cellular burden. Clusters of GV protein interactions are revealed, which establishes the plausible protein complexes important for the assembly process of these protein organelles. We anticipate our findings will set the stage for solving the molecular mechanism of GV assembly and designing GVs that efficiently assemble in heterologous hosts during biomedical applications.

synthetic biology↗

bioRxiv2023

Spatial Organization of Gas Vesicles is Governed by Phase-separable GvpU

Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy, and the recent engineering of GVs has led to multiple applications including reporter gene imaging, acoustic control, and payload delivery. GVs often cluster into a honeycomb pattern to minimize their occupancy of cytosolic space; however, the molecular mechanism behind this process and its influence on cellular physiology remain unknown. Here, we identified GvpU as the protein governing this process. GvpU-mediated clustering is selective to the genotype of GVs, allowing the design of GV variants with genetically encodable clustering states. Furthermore, we uncovered that the clustering is modulated by phase transition behaviors encoded in the intrinsically disordered region of GvpU through a balanced contribution of acidic and aromatic residues, and such phase transition can directly modulate cellular fitness. Collectively, our findings elucidate the protein player, molecular mechanism, and functional roles of GV clustering, and its programmability for biomedical applications.

synthetic biology↗