The protein shells of bacterial microcompartment organelles
Graphical abstract
Research highlights
► Many bacteria contain protein-based organelles for special metabolic functions. ► The shells of these proteinaceous organelles are reminiscent of viral capsids. ► The basic building blocks of the shells are hexameric proteins with central pores. ► Metabolic substrates and products are believed to diffuse through the pores. ► Structural studies of the shell proteins illustrate their mechanistic sophistication.
Introduction
Many bacteria contain large, polyhedral, protein-based organelles referred to as bacterial microcompartments (reviewed in [1, 2, 3, 4]). Polyhedral inclusions that had been visualized by electron microscopy in cyanobacteria and some chemoautotrophs were first isolated in 1973 and determined to contain the CO2-fixing enzyme RuBisCO [5••]; they were therefore named carboxysomes, and are now recognized as the founding member of a diverse group of microcompartments (Figure 1). Subsequent genetic and physiological studies on carboxysomes indicated that they played an active role in CO2 fixation [6, 7, 8, 9]. As part of a mechanism for enhancing CO2 fixation, carbonic anhydrase, which dehydrates bicarbonate to CO2, is encapsulated in the carboxysome together with RuBisCO [10•, 11, 12]. This arrangement is believed to provide a high concentration of CO2 for RuBisCO under growth conditions where inorganic carbon is limiting, and may confer other advantages as well [13]. Besides the carboxysome, several other types of bacterial microcompartments carrying out more complex reactions have been either studied directly or inferred from genomic data.
A unifying feature of diverse bacterial microcompartments is a thin shell composed primarily of a few thousand small protein subunits belonging to a family of homologous so-called BMC (for bacterial microcompartment) shell proteins. This outer shell encapsulates the interior enzymes while allowing transport of substrates and products. BMC shell proteins, which were first identified in carboxysomes [14, 15•, 16], were subsequently identified in the propanediol utilization operon (pdu) of Salmonella (a heterotroph) [17, 18••]. Genetic and biochemical studies demonstrated that the Pdu microcompartment encapsulates a series of enzymes that metabolize 1,2-propanediol (1,2-PD) [19•, 20] (Figure 1). Sequestering that metabolic pathway prevents exposure of the cytosol to propionaldehyde — an intermediate in the reaction pathway — which is toxic to the cell at high concentrations [20, 21]. Likewise, genes for BMC shell proteins are found in an operon for metabolizing ethanolamine in enteric bacteria [22, 23], including Salmonella and Escherichia coli. The ethanolamine utilization (or Eut) microcompartment system shares similar chemistry and analogous enzymes with the Pdu system. Experiments on the Eut system in Salmonella indicate that the sequestered metabolism of ethanolamine prevents exposure of the cytosol to the reactive acetaldehyde intermediate [24], while also preventing the detrimental evaporative loss of that compound from the cell [25]. Compared to the carboxysome, the latter two types of microcompartments are more complex. Besides encapsulating more enzymes, the interior reactions involve numerous cofactors, including adenosyl cobalamin (B12), NAD+/NADH, acetyl-CoA, ATP, and [Fe–S] clusters (reviewed in [1, 3]).
Motivated by the discovery of BMC shell proteins in diverse bacteria, searches for homologous shell proteins across the known protein sequence databases have emphasized the widespread occurrence of microcompartments across the bacterial kingdom, and their likely spread by horizontal gene transfer [2, 3, 4, 26, 27••]. Approximately 1700 unique proteins containing BMC domains can be identified at present, covering at least 10 different bacterial phyla. Multiple paralogs of the shell proteins are essentially always found together. Experimental studies on these wide ranging systems are limited, though inferences regarding their likely functions can be made in some cases from the genomic contexts in which the BMC shell proteins are found [2, 3]. Enzymes found to occur often in chromosomal proximity to BMC shell proteins have been tabulated [3]. These represent avenues for exploratory experimental work.
Until recently, the structure and mechanisms of bacterial microcompartment shells were unclear. At the architectural level, early electron microscopy studies on carboxysomes had not provided a definitive shape. Likewise, at the atomic level, three-dimensional details were lacking. How the shell proteins assembled to form a semi-permeable layer, and why multiple distinct paralogs are involved, were unknown. Crystal structures of numerous BMC shell proteins, first from the carboxysome [27••, 28••, 29••, 30, 31] and then from the Pdu [32•, 33•], Eut [34•, 35, 36••], and other systems [37•], have clarified how BMC shell proteins assemble to form a shell, how they might facilitate molecular transport through their pores, and how distinct paralogs play specialized roles in microcompartment organelles.
Section snippets
Elements of BMC shell protein assembly
The typical BMC domain is about 90 amino acids in length and adopts an alpha/beta fold ([27••], reviewed in [3]). Individual BMC proteins self-assemble to form cyclic, disc-shaped hexamers that constitute the basic building blocks of the shell (Figure 2). Each hexamer typically presents a narrow pore through the middle, along the six-fold axis of symmetry. Although individual BMC proteins differ, as described subsequently, in most cases the two sides of the disc reveal dramatically different
The roles of BMC protein fold variations
Crystal structures of numerous BMC proteins have revealed a surprising array of conformational and topological variations within a small protein domain (reviewed in [3]) (Table 1). Some BMC proteins are related to the canonical type by a circular permutation, so that a similar tertiary structure arises from secondary structures occurring in a different order [28••, 32•, 33•, 34•, 36••, 37•]. This produces N-termini and C-termini at different spatial locations, which may be an important feature.
Protein pores and molecular transport
The small pores visualized in the centers of typical BMC shell proteins are presumed to be the routes of transport for the substrates, products, and cofactors for varied microcompartments [27••, 30, 32•]. Size, electrostatic and hydrogen bonding features of the pores have been identified as potentially important in facilitating the transport of substrates and products more readily than the sequestered metabolic intermediates (Figure 3). BMC proteins that represent major components of their
Targeting enzymes to the shell interior
Some of the details concerning how enzymes are targeted to the interior surfaces of their respective microcompartments are beginning to emerge. Interestingly, at least two different kinds of mechanisms appear to operate in different microcompartments. In carboxysomes belonging to the so-called beta type, a highly unusual protein, CcmM, appears to serve as a scaffold for establishing interactions to both shell proteins and enzymes [49, 50]. CcmM bears an N-terminal domain that carries a
Open questions and future directions
Myriad questions remain concerning the function and evolution of bacterial microcompartments. Recent studies indicate that active cellular mechanisms may control the arrangement and movement of microcompartments in the cell [42•, 56], and that microcompartments may interact with other cellular components and inclusions [55]. Further studies are required to understand these cellular interactions. Likewise, little is known about how various enzymes are organized within microcompartments. Those
Conflict of interest
The authors declare no competing financial interests.
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
The authors thank Dr. Christopher Crowley for a critical reading of the manuscript. This work was supported by NIH grant AI081146 (TOY and TAB) and NSF grant MCB-0843065 (TOY). MCT is supported by a Ruth L. Kirschstein National Research Service Award GM007185.
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