The Carboxysome Shell Is Permeable to Protons

Abstract

Bacterial microcompartments (BMCs) are polyhedral organelles found in an increasingly wide variety of bacterial species. These structures, typified by carboxysomes of cyanobacteria and many chemoautotrophs, function to compartmentalize important reaction sequences of metabolic pathways. Unlike their eukaryotic counterparts, which are surrounded by lipid bilayer membranes, these microbial organelles are bounded by a thin protein shell that is assembled from multiple copies of a few different polypeptides. The main shell proteins form hexamers whose edges interact to create the thin sheets that form the facets of the polyhedral BMCs. Each hexamer contains a central pore hypothesized to mediate flux of metabolites into and out of the organelle. Because several distinctly different metabolic processes are found in the various BMCs studied to date, it has been proposed that a common advantage to packaging these pathways within shell-bound compartments is to optimize the concentration of volatile metabolites in the BMC by maintaining an interior pH that is lower than that of the cytoplasm. We have tested this idea by recombinantly fusing a pH-sensitive green fluorescent protein (GFP) to ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the major enzyme component inside the carboxysome. Our results suggest that the carboxysomal pH is similar to that of its external environment and that the protein shell does not constitute a proton barrier. The explanation for the sundry BMC functions must therefore be sought in the characteristics of the pores that traverse their shells.Clearly, the subcellular organization of bacteria is much more complex than was once assumed (reviewed in references 17 and 26), and many bacteria are able to compartmentalize metabolic processes into distinct organelles. Among these, the bacterial microcompartments (BMCs) have garnered attention because the genetic potential to form these structures, which consist entirely of protein, is widespread among the bacteria (1). BMCs have been credited with enhancing the activity of the enzyme(s) they contain by providing a unique environment with optimized substrate concentrations or pH, facilitating metabolite channeling, or protecting the cell by sequestering toxic intermediates (1). Based on comparative genomic and biochemical analyses, the interiors of BMCs in various bacteria are populated by different complements of enzymes, suggesting that, collectively, these organelles play a role in a multitude of metabolic pathways. The bounding shells of all BMCs, on the other hand, appear to be built from multimeric assemblies of proteins that belong to the same two families (pfam 00936 and pfam 03319) (7,11,12,29,30,32). Despite some structural differences between individual members of the two main shell protein types, the central pores in the pentamers and hexamers formed by these proteins have been implicated in mediating metabolite traffic across the BMC shell and, in some cases, may actively regulate transfer of substrates and products across the ...

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“…S1). The addition of GFP tag might limit the number of Rubisco proteins accommodated within the carboxysomal interior (Menon et al, 2010). Thus, there seems to be a regulation to avert full segregation and retain some unlabeled Rubisco in the carboxysome.…”

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“…4). The pH in the carboxysome will most likely be the same as in the stroma, since protons can readily cross the carboxysome shell (Menon, 2010), so altering carboxysomal pH would require changing stromal pH as well. However, it is not known how the diffusion of protons within the lattice of Rubisco will affect pH in the carboxysome.…”

pH determines the energetic efficiency of the cyanobacterial CO 2 concentrating mechanism

“…It has been suggested that the carboxysome might maintain a pH gradient, with the cytosolic and carboxysomal pHs differing (37,52). Altering the pH in the carboxysome would influence CCM efficiency in two ways.…”

“…S11), emphasizing that quantitation of these permeability values is vital to understanding the cyanobacterial CCM. We further assume the cytosolic and carboxysomal pH are equal based on the observation of fast pH equilibration across the α-carboxysome shell (52). However, it may be possible for the CCM to maintain a ΔpH across the carboxysome shell (SI Appendix).…”