Abstract
Bacterial microcompartments (BMCs) are protein-based organelles that expand the metabolic potential of many bacteria by sequestering segments of enzymatic pathways in a selectively permeable protein shell. Sixty-eight different types/subtypes of BMCs have been bioinformatically identified based on the encapsulated enzymes and shell proteins encoded in genomic loci. BMCs are found across bacterial phyla. The organisms that contain them, rather than strictly correlating with specific lineages, tend to reflect the metabolic landscape of the environmental niches they occupy. From our recent comprehensive bioinformatic survey of BMCs found in genome sequence data, we find many in members of the human microbiome. Here we survey the distribution of BMCs in the different biotopes of the human body. Given their amenability to be horizontally transferred and bioengineered they hold promise as metabolic modules that could be used to probiotically alter microbiomes or treat dysbiosis.
Highlights
Bacterial Microcompartments (BMCs) are organelles that are functionally similar to those of eukaryotes; they establish and contain a microenvironment that is distinct from the rest of the cell (Kerfeld et al, 2018; Kirst and Kerfeld, 2019)
Ethanolamine is abundant in the inflamed gut and the presence of tetrathionate as the electron acceptor allows for intestinal pathogens such as Salmonella enterica, Enterococcus faecalis, enterohaemorrhagic Escherichia coli (EHEC), Clostridium difficile to flourish by utilizing ethanolamine utilization (EUT) BMCs (Bertin et al, 2011; Srikumar and Fuchs, 2011; Thiennimitr et al, 2011; Anderson et al, 2018; Ormsby et al, 2019)
In many ecosystems the BMCs employed by community members reflect important characteristics of the nutritional landscape of the environmental niche, such as the importance of the PVM BMC (Planctomycete and Verrucomicrobia microcompartment) for the degradation of complex polysaccharides originating from algae (Erbilgin et al, 2014; Sichert et al, 2020; Sizikov et al, 2020)
Summary
Bacterial Microcompartments (BMCs) are organelles that are functionally similar to those of eukaryotes; they establish and contain a microenvironment that is distinct from the rest of the cell (Kerfeld et al, 2018; Kirst and Kerfeld, 2019). The purpose of the BMC shell in these metabolosomes is to enhance catalysis and sequester toxic aldehyde intermediates (Figure 1B) (Kerfeld et al, 2018). The EUT operon is part of the core E. coli genome (Dadswell et al, 2019), allowing the organism to use ethanolamine as a source of both carbon and Microcompartment Distribution in the Human Microbiome nitrogen (Kaval and Garsin, 2018). Because it is an environment with a large spectrum of available substrates known to be catabolized within BMCs, they are frequently found in gut microbes (Ravcheev et al, 2019)
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