Self-Assembly Stability and Variability of Bacterial Microcompartment Shell Proteins in Response to the Environmental Change
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.
KeywordsBacterial microcompartment Protein dynamics Self-assembly High-speed atomic force microscopy Synthetic engineering
Bacterial microcompartment hexamer
Bacterial microcompartment pentamer
Bacterial microcompartment trimer
Dynamic light scattering
- E. coli
High-speed atomic force microscopy
Specific protein-protein interactions ensure the self-assembly of BMC proteins to form highly defined architectures to fulfill their metabolic functionality. The lateral interactions between shell proteins are assumed to be the major factor for determining the self-assembly properties of the icosahedral shell . It has been observed that BMC-H homologs can form various shapes, including two-dimensional sheets [11, 12], nanotubes [13, 14, 15, 16, 17], and filament structures [15, 18, 19, 20].
Based on the self-assembly, selective permeability and enzyme encapsulation properties of the naturally occurring organelles, BMCs have been considered as an ideal system with great potential in bioengineering, including bioinspired construction of nanoscale bioreactors by encasing metabolic enzymes and generation of new molecular scaffolds with new functions [21, 22, 23, 24, 25, 26]. However, some key issues remain to be tackled in BMC bioengineering, for example, how stable the BMC structures are and how to manipulate and assess effectively the self-assembly and formation of BMC protein aggregates. Investigations of the structures and assembly of BMC shells and entire BMCs have been carried out using X-ray crystallography, electron microscopy (EM), fluorescence microscopy, and dynamic light scattering (DSL) [10, 11, 16, 22, 27, 28, 29, 30, 31]. Recently, we have exploited high-speed AFM (HS-AFM) to conduct the first visualization of the dynamic self-assembly process of BMC-H proteins .
In this work, we use HS-AFM to monitor the structural dynamics of BMC-H patches under varying pH and ionic conditions, which provides insight into the modulation of BMC shell protein assembly and offers a powerful tool for quantitative assessment, at the molecular resolution, on the stability and variability of BMC shell protein self-assembly.
The purified BMC-H protein (Hoch_5815) from Haliangium ocraceum was kindly provided by Dr. Kerfeld (Lawrence Berkeley National Laboratory). For buffer exchange, stock samples at ~ 80 mg mL−1 in Tris buffer (50 mM Tris-HCl, pH 7.8, 100 mM KCl, 10 mM MgCl2) were diluted to 0.5 mg mL−1 using the desired buffer prior to AFM imaging (Additional file 1: Figure S1). The control buffer is 50-mM Tris-HCl (pH 7.8) and 10 mM MgCl2.
Atomic Force Microscopy
Desired buffers were used for sample absorption on mica and AFM imaging. After 5 min absorption on the mica, Hoch_5815 were rinsed with the desired buffer to remove immobilized proteins and then imaged using AFM (Additional file 1: Figure S1). HS-AFM images were captured at 30 or 40 Hz in solution in AC mode using a JPK NanoWizard ULTRA speed AFM equipped with an ULTRA Speed 2.8 μm scanner and Ultra-Short Cantilever USC-0.3 MHz probes (NanoWorld). Minimal loading forces of ~ 100 picoNewton were applied during AFM imaging to reduce disturbance of protein assembly [12, 32, 33, 34, 35, 36].
Image Processing and Analysis
where N represents the sum of white and black pixels in a thresholded difference image divided by the number of pixels corresponding to a single hexamer at that scale (Additional file 1: Figure S3, Figure S5). Data is presented as mean ± standard deviation (SD). Statistical analysis was performed using multivariate ANOVA or two-way ANOVA as specified.
We used the BMC-H proteins (Hoch_5815) from a myxobacterium Haliangium ocraceum, which were expressed in Escherichia coli and characterized as hexamers with a six-fold symmetry . Hoch_5815 hexamers could self-assemble to form single-layered sheets at the second timescale, which represent the basic structural components of the icosahedral BMC architecture (Fig. 1a). HS-AFM imaging allows us to visualize the dynamic assembly and organizational flexibility of sheet fragments (Fig. 1b) and quantitatively estimate the patch size and dynamic rate of BMC-H proteins using the developed imaging analysis (see the “Methods” section).
Response to pH Variation
AFM imaging on the self-assembly of Hoch_5815 proteins in shell sheets has revealed that the formation of shell sheets is ascribed to a combination of the assembly and disassembly of hexamers . We further examined the rates of Hoch_5815 self-assembly dynamics and dynamic events under different pH (Additional file 1: Table S2) to explore the stability of Hoch_5815 protein-protein interactions. The rate of self-assembly dynamics is the highest at pH 7 and decreases in both acidic and alkaline conditions (Fig. 2b; Additional file 1: Figure S3). In particular, it declines rapidly in acidic conditions, notably from pH 7 to pH 6 and appears relatively constant between pH 4 and pH 3, as shown in Fig. 2b.
It is likely that pH has a great impact on the electrostatic properties of amino acid residues located at the hexamer-hexamer interface. The decreased dynamics and a smaller size of shell patches observed in acidic conditions illustrate that Hoch_5815 has a reduced self-assembling ability. The reduced dynamics and a larger size of shell patches observed in the alkaline conditions suggest stable hexamer-hexamer interactions, whereas the increased dynamics of Hoch_5815 hexamers imply flexible hexamer-hexamer interactions in the neutral pH condition.
Response to the Variation of Salt Concentrations
Moreover, the variations of Hoch_5815 self-assembly caused by the changes in MgCl2 and KCl concentrations are relatively similar. By contrast, the change in patch size is most pronounced (up to a 3000-fold increase) when the CaCl2 concentration is raised from 200 to 300 mM (Fig. 3a), suggesting the higher sensitivity of Hoch_5815 self-assembly to CaCl2 than to MgCl2 or KCl.
The dynamic rate of Hoch_5815 self-assembly is also affected by changes in the buffer salt concentration. The increase in MgCl2, CaCl2, or KCl concentrations could result in the decline of the Hoch_5815 dynamic rate (Fig. 3b; Additional file 1: Figure S5). Given the increase in the patch size observed under higher salt concentrations (Fig. 3a), it appears that the lateral interactions between Hoch_5815 hexamers are more stable under high salt concentrations. Changes in CaCl2 concentration had a more pronounced response, and there was a significant shift in the rate of dynamic events between 200 and 300 mM (Fig. 3b), whereas the responses to the changes in MgCl2 and KCl are relatively similar, consistent with the changes in the patch size (Fig. 3a). Interestingly, the highest proportions of assembly events versus disassembly events were observed under 400 mM of MgCl2, CaCl2, or KCl (Additional file 1: Table S2). This led to the formation of large and stable single-layer Hoch_5815 assemblies under 400 mM salt (Additional file 1: Figure S4). The double-layer assemblies observed at 500 mM are also stable and exhibit low rates of hexamer movement.
Flexibility of BMC-H Protein Assembly
BMCs comprise hundreds of proteins that self-assemble to form the higher ordered structures. The BMC shell, consisting of numerous protein homologs, is an ideal system for studying protein self-assembly and interactions. As a powerful technique for analyzing biomembrane organization, protein assembly, and physical interactions that are highly relevant to the physiological roles of biological systems [32, 35, 38, 39], AFM has been exploited to visualize the organization and self-assembly dynamics of BMC shell proteins and the architectures and mechanical features of BMC structures [12, 30, 31, 40, 41, 42]. This work represents, to our knowledge, the first quantitative determination of the self-assembly dynamics of BMC shell proteins in the formation of two-dimensional sheets in response to environmental changes using AFM. The results highlight the inherent variability and environmental dependence of BMC-H protein self-assembly. Compared with EM and DSL, AFM exhibits great potential in monitoring the dynamic actions of BMC protein self-assembly in real time with molecular details.
Protein-protein interactions are of significant importance in forming and shaping the BMC shell . The protein concentration has also been documented as a critical factor for driving shell formation [41, 43]. In addition, in vitro solubility studies have illustrated that pH and ionic strength in solution could influence the structural stability of BMCs [17, 27] as well as the assembly behaviors of BMC shell proteins in the formation of two-dimensional sheets [37, 41], nanotubes [13, 17], and nanocages , reminiscent of their impact on virus capsid assembly [44, 45]. We also found protein precipitation and no patches formed when pH > 10 and < 3 or the salt concentration < 10 mM or > 600 mM (unpublished data). Here, we further showed that the assembly tendency and dynamics are dependent on pH and salt concentration. Though shell proteins can self-assemble at a wide range of pH, the neutral pH environment appears to be capable of enhancing the assembly dynamics (Fig. 2b). Cations with a concentration of ≥ 300 mM were found to promote the formation of two-dimensional sheets; 400 mM cations appear to be desirable for the formation of large and stable single-layered sheets (Fig. 3). These conditions align with the cytosolic conditions of bacterial cells and are physiologically relevant. For example, under most physiologically relevant conditions, the pH of the E. coli cytosol is approximately 7.4–7.8  and the ion concentration is approximately 100–400 mM, which is vital for protein interactions, protein-ligand binding, signaling, maintaining membrane electrostatic potentials, and protein gradient across membranes [47, 48]. Although how interactions between samples and the mica substrate affect the self-assembly of BMC proteins remains to be further investigated, AFM imaging provides the opportunity for us to quantitatively analyze the dynamic changes of BMC protein self-assembly in response to environmental variations.
The environment-dependent assembly dynamics of BMC proteins in the formation of shell fragments described here might represent their behaviors in the formation of the entire BMC. In fact, the 3D BMC structures appear to be the dynamically maintained organelles designed in nature. BMCs present notable structural flexibility and heterogeneity; the mechanical softness of BMC shell structures determined by AFM nanoindentation  and the nonequilibrium dynamics of BMC assembly revealed by computational simulations  highlighted the differences between BMC and robust virus assemblies. Likewise, the biosynthesis of carboxysomes has been elucidated to correlate with light and chaperons [50, 51]. Very recently, it has been indicated that CcmK3 and CcmK4 can form heterohexamers and cap on the carboxysome shell in a pH-dependent manner, possibly providing a means for regulating carboxysome shell permeability and CO2 assimilation in the highly dynamic microenvironment . The exact mechanism underlying how environmental conditions in solution affect the thermodynamic assembly of BMC proteins remains to be investigated, for example, using a combination of experimental studies and computational simulations.
Given the self-assembly of BMC structures, there is a significant interest in engineering BMCs and design of new BMC-based nanobioreactors, molecular scaffolds, and biomaterials in biotechnology applications, for example, enhancing cell metabolism, enzyme encapsulation, molecular delivery, and therapy. Advanced knowledge about the structural resilience and variability of BMCs in response to environmental changes will not only inform strategies for producing robust BMC-based nanostructures in heterologous hosts, i.e., E. coli or plants [31, 53, 54], but also pave the way for modulating the formation of 2D nanomaterials as well as the opening and closure of BMC shell-based protein cages, thereby facilitating the functional regulation and targeted molecular delivery. Previously, we have demonstrated the feasibility of using genetic modification approach to manipulate the specific contacts at the interfaces of shell proteins and their self-assembly behaviors . This study strengthens our toolbox for assessing and manipulating BMC shell self-assembly in varying environments.
In summary, we exploited HS-AFM to carry out the quantitative investigations of BMC shell protein self-assembly under different pH and salt conditions. Formation of larger single-layered patches of shell hexamers was shown to be promoted at 400-mM salt concentration, and neutral pH resulted in a higher dynamic rate of hexamer self-assembly. The organizational transition of shell proteins from hexameric assemblies to fiber-like arrays was also visualized. This study illustrated that environmental conditions play an important role in determining the organization and self-assembly of BMC shell proteins.
The authors thank Dr Kerfeld (Lawrence Berkeley National Laboratory, US) for kindly providing the BMC-H Hoch_5815 proteins and thank the Centre for Cell Imaging at the University of Liverpool for BioAFM technical assistance (funded by Biotechnology and Biological Sciences Research Council, BB/M012441/1).
This research was supported by Royal Society (UF120411, RG130442, IE131399, URF\R\180030, RGF\EA\180233, to L.-N.L.) and Biotechnology and Biological Sciences Research Council Grants (BB/M024202/1, BB/R003890/1, to L.-N.L.).
Availability of Data and Materials
We declared that the materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes, without breaching participant confidentiality.
MF and L-NL performed the experiments. MF and L-NL conceived and designed the experiments. MF, LZ, SB, and L-NL analyzed the data. MF and L-NL wrote the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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