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

Selective molecular transport across the protein shells of bacterial microcompartments

Bacterial microcompartments are widespread organelles that play important roles in the environment and are associated with a number of human diseases. A key feature of bacterial MCPs is a selectively permeable protein shell that mediates the movement of substrates, products and cofactors in and out. Here we discuss current knowledge of selective transport across the protein shells of bacterial MCPs, including mechanisms, regulation and unanswered questions.

Protein stoichiometry, structural plasticity and regulation of bacterial microcompartments

Bacterial microcompartments (BMCs) are self-assembling prokaryotic organelles consisting of a polyhedral proteinaceous shell and encapsulated enzymes that are involved in CO₂ fixation or carbon catabolism. Addressing how the hundreds of building components self-assemble to form the metabolically functional organelles and how their structures and functions are modulated in the extremely dynamic bacterial cytoplasm is of importance for basic understanding of protein organelle formation and synthetic engineering of metabolic modules for biotechnological applications. Here, we highlight recent advances in understanding the protein composition and stoichiometry of BMCs, with a particular focus on carboxysomes and propanediol utilization microcompartments. We also discuss relevant research on the structural plasticity of native and engineered BMCs, and the physiological regulation of BMC assembly, function and positioning in native hosts.

Biophysical approaches to understand and re-purpose bacterial microcompartments

Bacterial microcompartments represent a modular class of prokaryotic organelles associated with metabolic processes. They harbor a congregation of enzymes that work in cascade within a small, confined volume. These sophisticated nano-engineered crafts of nature offer a tempting paradigm for the fabrication of biosynthetic nanoreactors. Repurposing bacterial microcompartments to develop nanostructures with desired functions requires a careful manipulation in their structural makeup and composition. This calls for a comprehensive understanding of all the interactions of the physical components which frame such molecular architectures. Over recent years, several biophysical techniques have been essential in illuminating the role played by bacterial microcompartments within cells, and have revealed crucial details regarding the morphology, physical properties and functions of their constituent proteins. This has promoted contemplation of ideas for engineering microcompartments inspired biomaterials with novel features and functions.

Recent structural insights into bacterial microcompartment shells

Bacterial microcompartments are organelle-like structures that enhance a variety of metabolic functions in diverse bacteria. Composed entirely of proteins, thousands of homologous hexameric shell proteins tesselate to form facets while pentameric proteins form the vertices of a polyhedral shell that encapsulates various enzymes, substrates and cofactors. Recent structural data have highlighted nuanced variations in the sequence and topology of microcompartment shell proteins, emphasizing how variation and specialization enable the construction of complex molecular machines. Recent studies engineering synthetic miniaturized microcompartment shells provide additional frameworks for dissecting principles of microcompartment structure and assembly. This review updates our current understanding of bacterial microcompartment shell proteins, providing new insights and highlighting outstanding questions.

Positioning the Model Bacterial Organelle, the Carboxysome

Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.

New discoveries expand possibilities for carboxysome engineering

Carboxysomes are CO₂-fixing protein compartments present in all cyanobacteria and some proteobacteria. These structures are attractive candidates for carbon assimilation bioengineering because they concentrate carbon, allowing the fixation reaction to occur near its maximum rate, and because they self-assemble in diverse organisms with a set of standard biological parts. Recent discoveries have expanded our understanding of how the carboxysome assembles, distributes itself, and sustains its metabolism. These studies have already led to substantial advances in engineering the carboxysome and carbon concentrating mechanism into recombinant organisms, with an eye towards establishing the system in industrial microbes and plants. Future studies may also consider the potential of in vitro carboxysomes for both discovery and applied science.

Mechanisms of Scaffold-Mediated Microcompartment Assembly and Size Control

This article describes a theoretical and computational study of the dynamical assembly of a protein shell around a complex consisting of many cargo molecules and long, flexible scaffold molecules. Our study is motivated by bacterial microcompartments, which are proteinaceous organelles that assemble around a condensed droplet of enzymes and reactants. As in many examples of cytoplasmic liquid-liquid phase separation, condensation of the microcompartment interior cargo is driven by flexible scaffold proteins that have weak multivalent interactions with the cargo. Our results predict that the shell size, amount of encapsulated cargo, and assembly pathways depend sensitively on properties of the scaffold, including its length and valency of scaffold-cargo interactions. Moreover, the ability of self-assembling protein shells to change their size to accommodate scaffold molecules of different lengths depends crucially on whether the spontaneous curvature radius of the protein shell is smaller or larger than a characteristic elastic length scale of the shell. Beyond natural microcompartments, these results have important implications for synthetic biology efforts to target alternative molecules for encapsulation by microcompartments or viral shells. More broadly, the results elucidate how cells exploit coupling between self-assembly and liquid-liquid phase separation to organize their interiors.

Advances in the World of Bacterial Microcompartments

Bacterial microcompartments (MCPs) are extremely large (100-400 nm) and diverse proteinaceous organelles that compartmentalize multistep metabolic pathways, increasing their efficiency and sequestering toxic and/or volatile intermediates. This review highlights recent studies that have expanded our understanding of the diversity, structure, function, and potential biotechnological uses of MCPs. Several new types of MCPs have been identified and characterized revealing new functions and potential new associations with human disease. Recent structural studies of MCP proteins and recombinant MCP shells have provided new insights into MCP assembly and mechanisms and raised new questions about MCP structure. We also discuss recent work on biotechnology applications that use MCP principles to develop nanobioreactors, nanocontainers, and molecular scaffolds.

Bacterial metabolosomes: new insights into their structure and bioengineering

Bacterial metabolosomes have been discovered for over 25 years. They play essential roles in bacterial metabolism and pathogenesis. In this crystal ball paper, I will discuss the recent advances in the fundamental understanding and synthetic engineering of bacterial metabolosomes.

Liquid-Liquid Phase Separation by Intrinsically Disordered Protein Regions of Viruses: Roles in Viral Life Cycle and Control of Virus-Host Interactions

Intrinsically disordered proteins (IDPs) are unable to adopt a unique 3D structure under physiological conditions and thus exist as highly dynamic conformational ensembles. IDPs are ubiquitous and widely spread in the protein realm. In the last decade, compelling experimental evidence has been gathered, pointing to the ability of IDPs and intrinsically disordered regions (IDRs) to undergo liquid-liquid phase separation (LLPS), a phenomenon driving the formation of membrane-less organelles (MLOs). These biological condensates play a critical role in the spatio-temporal organization of the cell, where they exert a multitude of key biological functions, ranging from transcriptional regulation and silencing to control of signal transduction networks. After introducing IDPs and LLPS, we herein survey available data on LLPS by IDPs/IDRs of viral origin and discuss their functional implications. We distinguish LLPS associated with viral replication and trafficking of viral components, from the LLPS-mediated interference of viruses with host cell functions. We discuss emerging evidence on the ability of plant virus proteins to interfere with the regulation of MLOs of the host and propose that bacteriophages can interfere with bacterial LLPS, as well. We conclude by discussing how LLPS could be targeted to treat phase separation-associated diseases, including viral infections.

Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production

Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biological elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diameter) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the production of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen production of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions.

The extreme oxygen sensitive character of hydrogenases is a longstanding issue for hydrogen production in bacteria. Here, the authors build carboxysome shells in E. coli and incorporate catalytically active hydrogenases and functional partners within the empty shell for the production of hydrogen.