Self-Assembly Stability and Variability of Bacterial Microcompartment Shell Proteins in Response to the Environmental Change

Abstract

Bacterial microcompartments (BMCs) are proteinaceous self-assembling organelles that are widespread among the prokaryotic kingdom. By segmenting key metabolic enzymes and pathways using a polyhedral shell, BMCs play essential roles in carbon assimilation, pathogenesis, and microbial ecology. The BMC shell is composed of multiple protein homologs that self-assemble to form the defined architecture. There is tremendous interest in engineering BMCs to develop new nanobioreactors and molecular scaffolds. Here, we report the quantitative characterization of the formation and self-assembly dynamics of BMC shell proteins under varying pH and salt conditions using high-speed atomic force microscopy (HS-AFM). We show that 400-mM salt concentration is prone to result in larger single-layered shell patches formed by shell hexamers, and a higher dynamic rate of hexamer self-assembly was observed at neutral pH. We also visualize the variability of shell proteins from hexameric assemblies to fiber-like arrays. This study advances our knowledge about the stability and variability of BMC protein self-assemblies in response to microenvironmental changes, which will inform rational design and construction of synthetic BMC structures with the capacity of remodeling their self-assembly and structural robustness. It also offers a powerful toolbox for quantitatively assessing the self-assembly and formation of BMC-based nanostructures in biotechnology applications. Electronic supplementary material The online version of this article (10.1186/s11671-019-2884-3) contains supplementary material, which is available to authorized users.

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein

“…It remains to be tested whether cations could transit through the CcmK2 pore or the pores of other shell proteins i.e. CcmK3, CcmK4 and CcmL, or through the gaps surrounding shell proteins generated by specific protein arrangement 34 and dynamic self-assembly and interactions 25,50 .…”

Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment

“…Variations in the diameter of intact carboxysomes, ranging from 90 to 600 nm, have been also shown in previous studies not only in single species but also among distinct species (Shively et al, 1973;Price and Badger, 1991;Iancu et al, 2007;Liberton et al, 2011), suggesting the adaptation strategies exploited by cyanobacteria for regulating their CO 2 -fixing machines to survive in diverse niches. It may be related to the environment-sensitive protein-protein interactions that drive protein self-assembly and BMC formation (Faulkner et al, 2019). Moreover, the spatial positioning and mobility of b-carboxysomes in live cells appear to be independent of carboxysome diameter but show a strong dependence to light intensity, suggesting that light-dependent mechanisms might mediate carboxysome location and diffusion.…”

“…Carboxysomes, although structurally resembling virus capsids, have been shown to be mechanically softer than the P22 virus capsid by a factor of ;10, suggesting greater flexibility of proteinprotein interactions within the carboxysome structure (Faulkner et al, 2017). The capping flexibility of pentamers may represent the dynamic nature of shell assembly probably in the second timescale and tunable protein-protein interactions in the shell, as characterized recently (Sutter et al, 2016;Faulkner et al, 2019).…”

Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment

“…Carboxysomes, though structurally resembling virus capsids, have been shown to be mechanically softer than the P22 virus capsid by a factor of ~10, suggesting greater flexibility of protein-protein interactions within the carboxysome structure (Faulkner et al, 2017). The capping flexibility of pentamers may represent the dynamic nature of shell assembly probably in the second timescale and tunable protein-protein interactions in the shell, as characterized recently (Sutter et al, 2016;Faulkner et al, 2019).…”