Bacterial microcompartments

Abstract

Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.

Figure 1. Core biochemistry of carboxysomes and metabolosomes and superloci organization

A) Schematic of the bacterial microcompartment (BMC) shell and encapsulated enzymes and associated flow of substrates/products. α-carboxysomes and β-carboxysomes both encapsulate carbonic anhydrase (CA) and Form 1 RuBisCO to fix CO₂ as part of the Calvin-Benson-Bassham Cycle (CBB). The shell prevents loss of CO2 to the cytoplasm. B) Metabolosomes have more diverse initial substrates compared to carboxysomes, but they typically share a common core biochemistry that is based on a signature enzyme, an aldehyde dehydrogenase (AldDH), an alcohol dehydrogenase (AlcDH) and a phosphotransacylase (PTAC). The signature enzyme generates the aldehyde which is then converted to a product alcohol by the AlcDH. This reaction uses CoA and NAD+ which are recycled in a separate reaction branch that uses AldDH and PTAC to produce a phosphorylated product (R-P). This product is then dephosphorylated by an acetyl kinase (AK) in a reaction that generates ATP. C) Schematic of a typical gene composition in a superlocus encoding a BMC. In addition to genes encoding shell and core proteins, BMC superloci encode proteins for supporting and ancillary functions, like transporters for the signature substrate. 3-PGA, 3-phosphoglycerate; RuBP, ribulose 1,5-bisphosphate;.

Figure 2. Overview of BMCs in different phyla and tree of shell pentamers

A) Bacterial phyla tree with distribution of bacterial microcompartment (BMC) locus types. Locus types, excluding satellite and satellite-like loci, denoted as colored shapes are adjacent to the phyla in which they appear. For a given phylum, the shape of the triangular wedge represents sequence diversity; the nearest edge represents the shortest branch length from the phylum node to a leaf, while the farthest edge represents the longest branch length from the phylum node to a leaf. Reproduced with permission from REF. B) Phylogenetic tree of BMC-P shell proteins (which occupies the vertex position of BMC shells) shows a large distance between α-carboxysomal and β-carboxysomal homologs. β-carboxysomal BMC-P proteins are more closely related to their counterparts in the metabolosomes of heterotrophic organisms than to the BMC-P proteins of α-carboxysomes. To construct the tree, amino acid sequences were identified in the Uniprot RP75 database with a Hidden Markov Model (HMM) of the BMC-P protein family (Pfam03319). The collected sequences were then made non-redundant with a cutoff of 95% identity, aligned and used to build the phylogenetic tree. Reproduced with permission from REF.

Figure 3. Schematics of BMC structure

A) Bacterial microcompartment (BMC) shells are made of three types of building blocks: BMC-H (blue), BMC-T (green) and BMC-P (yellow). BMC-T has two subtypes based on sequence and oligomer status: single layered BMC-T^s and double layered BMC-T^d. Pores (circles) and central axes of symmetry are shown in the space-filling orientations. B) Three building blocks tile together to form BMC shells. Overview of the Haliangium ochraceum (HO) whole shell and the highly conserved planar BMC-domain interactions as observed in the HO BMC shell structure and in the crystal packing of many other BMC-H structures. C) Position of the BMC-T in the shell, interfacing with two different BMC-H edges (planar and tilted, marked with red lines; icosahedral symmetry axis indicated with filled symbols, pseudosymmetry with open symbols, top layer of BMC-T omitted for clarity).

Figure 4. Schematics of bacterial microcompartment (BMC) assembly pathways

A) Core first assembly: core proteins coalesce through protein domain interactions or aggregation of encapsulation peptides. Encapsulation peptides interact with shell proteins which then form the shell around the core. B) Concomitant assembly: core and shell proteins assemble together with the help of core assembly proteins.

Figure 5. Example of strategies to design synthetic bio-nanoreactors and scaffolding architectures using building blocks from bacterial microcompartments (BMCs)

The natural diversity of BMCs provides a rich collection of building blocks with specific functions, structures, permeability and enzymatic activity. New enzymatic functions can be targeted to the interior of the shell using encapsulation peptides and synthetic BMC cores can be engineered using protein fusions. Modifying the shell proteins enables altered permeability or the introduction of new functions such as electron transfer. Biomaterials, such as scaffolds for metabolic pathways, can also be constructed using the same strategies. Synthetic BMCs and scaffolds can be used in vivo and in vitro.