A Survey of Bacterial Microcompartment Distribution in the Human Microbiome

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.

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Clues to the function of bacterial microcompartments from ancillary genes

Biochemical Society Transactions ◽

10.1042/bst20200632 ◽

2021 ◽

Author(s):

Henning Kirst ◽

Cheryl A. Kerfeld

Keyword(s):

Metabolic Pathways ◽

Transmembrane Proteins ◽

Transcriptional Regulators ◽

Building Blocks ◽

Data Set ◽

Bacterial Phyla ◽

Bacterial Microcompartments ◽

Shell Proteins ◽

Regulation Mechanisms ◽

Protein Shell

Bacterial microcompartments (BMCs) are prokaryotic organelles. Their bounding membrane is a selectively permeable protein shell, encapsulating enzymes of specialized metabolic pathways. While the function of a BMC is dictated by the encapsulated enzymes which vary with the type of the BMC, the shell is formed by conserved protein building blocks. The genes necessary to form a BMC are typically organized in a locus; they encode the shell proteins, encapsulated enzymes as well as ancillary proteins that integrate the BMC function into the cell's metabolism. Among these are transcriptional regulators which usually found at the beginning or end of a locus, and transmembrane proteins that presumably function to conduct the BMC substrate into the cell. Here, we describe the types of transcriptional regulators and permeases found in association with BMC loci, using a recently collected data set of more than 7000 BMC loci distributed over 45 bacterial phyla, including newly discovered BMC loci. We summarize the known BMC regulation mechanisms, and highlight how much remains to be uncovered. We also show how analysis of these ancillary proteins can inform hypotheses about BMC function; by examining the ligand-binding domain of the regulator and the transporter, we propose that nucleotides are the likely substrate for an enigmatic uncharacterized BMC of unknown function.

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Engineered shell proteins confer improved encapsulated pathway behavior in a bacterial microcompartment

10.1101/106716 ◽

2017 ◽

Author(s):

Marilyn F. Slininger Lee ◽

Christopher M. Jakobson ◽

Danielle Tullman-Ercek

Keyword(s):

Growth Enhancement ◽

Shell Protein ◽

Bacterial Microcompartment ◽

Hydropathy Index ◽

Shell Proteins ◽

Structure Result ◽

Pore Lining ◽

Protein Shell ◽

Control Diffusion ◽

Do So

AbstractBacterial microcompartments are a class of proteinaceous organelles comprising a characteristic protein shell enclosing a set of enzymes. Compartmentalization can prevent escape of volatile or toxic intermediates, prevent off-pathway reactions, and create private cofactor pools. Encapsulation in synthetic microcompartment organelles will enhance the function of heterologous pathways, but to do so, it is critical to understand how to control diffusion in and out of the microcompartment organelle. To this end, we explored how small differences in the shell protein structure result in changes in the diffusion of metabolites through the shell. We found that the ethanolamine utilization (Eut) protein EutM properly incorporates into the 1,2-propanediol utilization (Pdu) microcompartment, altering native metabolite accumulation and the resulting growth on 1,2-propanediol as the sole carbon source. Further, we identified a single pore-lining residue mutation that confers the same phenotype as substitution of the full EutM protein, indicating that small molecule diffusion through the shell is the cause of growth enhancement. Finally, we show that the hydropathy index and charge of pore amino acids are important indicators to predict how pore mutations will affect growth on 1,2- propanediol, likely by controlling diffusion of one or more metabolites. This study highlights the success of two strategies to engineer microcompartment control over metabolite transport: altering the existing shell protein pore via mutation of the pore-lining residues, and generating chimeras using shell proteins with the desired pores.TOC Abstract Graphic

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Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x21007470 ◽

2021 ◽

Vol 77 (9) ◽

Author(s):

Jessica M. Ochoa ◽

Oscar Mijares ◽

Andrea A. Acosta ◽

Xavier Escoto ◽

Nancy Leon-Rivera ◽

...

Keyword(s):

Structural Characterization ◽

Building Blocks ◽

Type I ◽

Type Ii ◽

Protein Subunits ◽

Bacterial Microcompartments ◽

Bacterial Microcompartment ◽

Glycyl Radical ◽

Shell Proteins

Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I and type II choline-utilization microcompartments are reported. Sequence and structure analysis reveals electrostatic surface properties that are shared between the four types of shell proteins described here.

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In Salmonella enterica, Ethanolamine Utilization Is Repressed by 1,2-Propanediol To Prevent Detrimental Mixing of Components of Two Different Bacterial Microcompartments

Journal of Bacteriology ◽

10.1128/jb.00215-15 ◽

2015 ◽

Vol 197 (14) ◽

pp. 2412-2421 ◽

Cited By ~ 18

Author(s):

Ryan Sturms ◽

Nicholas A. Streauslin ◽

Shouqiang Cheng ◽

Thomas A. Bobik

Keyword(s):

Protein Interactions ◽

Regulatory Protein ◽

Gene Clusters ◽

Content Type ◽

Bacterial Microcompartments ◽

Shell Protein ◽

Bacterial Microcompartment ◽

Genes Encoding ◽

Shell Proteins ◽

High Conservation

ABSTRACTBacterial microcompartments (MCPs) are a diverse family of protein-based organelles composed of metabolic enzymes encapsulated within a protein shell. The function of bacterial MCPs is to optimize metabolic pathways by confining toxic and/or volatile metabolic intermediates. About 20% of bacteria produce MCPs, and there are at least seven different types. Different MCPs vary in their encapsulated enzymes, but all have outer shells composed of highly conserved proteins containing bacterial microcompartment domains. Many organisms have genes encoding more than one type of MCP, but given the high homology among shell proteins, it is uncertain whether multiple MCPs can be functionally expressed in the same cell at the same time. In these studies, we examine the regulation of the 1,2-propanediol (1,2-PD) utilization (Pdu) and ethanolamine utilization (Eut) MCPs inSalmonella. Studies showed that 1,2-PD (shown to induce the Pdu MCP) represses transcription of the Eut MCP and that the PocR regulatory protein is required. The results indicate that repression of the Eut MCP by 1,2-PD is needed to prevent detrimental mixing of shell proteins from the Eut and Pdu MCPs. Coexpression of both MCPs impaired the function of the Pdu MCP and resulted in the formation of hybrid MCPs composed of Eut and Pdu MCP components. We also show that plasmid-based expression of individual shell proteins from the Eut MCP or the β-carboxysome impaired the function of Pdu MCP. Thus, the high conservation among bacterial microcompartment (BMC) domain shell proteins is problematic for coexpression of the Eut and Pdu MCPs and perhaps other MCPs as well.IMPORTANCEBacterial MCPs are encoded by nearly 20% of bacterial genomes, and almost 40% of those genomes contain multiple MCP gene clusters. In this study, we examine how the regulation of two different MCP systems (Eut and Pdu) is integrated inSalmonella. Our findings indicate that 1,2-PD (shown to induce the Pdu MCP) represses the Eut MCP to prevent detrimental mixing of Eut and Pdu shell proteins. These findings suggest that numerous organisms which produce more than one type of MCP likely need some mechanism to prevent aberrant shell protein interactions.

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Selective molecular transport through the protein shell of a bacterial microcompartment organelle

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1423672112 ◽

2015 ◽

Vol 112 (10) ◽

pp. 2990-2995 ◽

Cited By ~ 72

Author(s):

Chiranjit Chowdhury ◽

Sunny Chun ◽

Allan Pang ◽

Michael R. Sawaya ◽

Sharmistha Sinha ◽

...

Keyword(s):

Small Molecules ◽

Carbon Fixation ◽

Molecular Diffusion ◽

Molecular Transport ◽

Phenotypic Data ◽

Bacterial Microcompartments ◽

Shell Protein ◽

Bacterial Microcompartment ◽

Selective Permeability ◽

Protein Shell

Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. Here, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.

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Self-assembling shell proteins PduA and PduJ have essential and redundant roles in bacterial microcompartment assembly

10.1101/2020.07.06.187062 ◽

2020 ◽

Author(s):

Nolan W. Kennedy ◽

Svetlana P. Ikonomova ◽

Marilyn Slininger Lee ◽

Henry W. Raeder ◽

Danielle Tullman-Ercek

Keyword(s):

Self Assembly ◽

Carbon Fixation ◽

Enteric Bacteria ◽

Bacterial Microcompartments ◽

Bacterial Microcompartment ◽

Self Assembling ◽

Assembly Mechanism ◽

High Propensity ◽

Serovar Typhimurium ◽

Shell Proteins

AbstractProtein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment from Salmonella enterica serovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.

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MCPdb: The bacterial microcompartment database

PLoS ONE ◽

10.1371/journal.pone.0248269 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248269

Author(s):

Jessica M. Ochoa ◽

Kaylie Bair ◽

Thomas Holton ◽

Thomas A. Bobik ◽

Todd O. Yeates

Keyword(s):

Tertiary Structure ◽

Protein Structures ◽

Structural Features ◽

Protein Subunits ◽

The Public ◽

Bacterial Microcompartments ◽

Bacterial Microcompartment ◽

Metabolic Functions ◽

Shell Proteins ◽

Metabolic Reactions

Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, the existing functionalities of current resources have limited our ability to rapidly understand the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphasize the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 163 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria.

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Computational and experimental approaches to controlling bacterial microcompartment assembly

10.1101/2021.01.18.427120 ◽

2021 ◽

Author(s):

Yaohua Li ◽

Nolan W. Kennedy ◽

Siyu Li ◽

Carolyn E. Mills ◽

Danielle Tullman-Ercek ◽

...

Keyword(s):

Self Assembly ◽

Bacterial Species ◽

Coarse Grained ◽

Bacterial Phyla ◽

Energy Applications ◽

Bacterial Microcompartments ◽

Bacterial Microcompartment ◽

Experimental Approaches ◽

Amino Acid Mutations ◽

Coarse Grained Simulations

AbstractBacterial microcompartments compartmentalize the enzymes that aid chemical and energy production in many bacterial species. These protein organelles are found in various bacterial phyla and are postulated to help many of these organisms survive in hostile environments such as the gut of their hosts. Metabolic engineers are interested in repurposing these organelles for non-native functions. Here, we use computational, theoretical and experimental approaches to determine mechanisms that effectively control microcompartment self-assembly. As a model system, we find via multiscale modeling and mutagenesis studies, the interactions responsible for the binding of hexamer-forming proteins propanediol utilization bacterial microcompartments from Salmonella and establish conditions that form various morphologies. We determine how the changes in the microcompartment hexamer protein preferred angles and interaction strengths can modify the assembled morphologies including the naturally occurring polyhedral microcompartment shape, as well as other extended shapes or quasi-closed shapes. We demonstrate experimentally that such altered strengths and angles are achieved via amino acid mutations. A thermodynamic model that agrees with the coarse-grained simulations provides guidelines to design microcompartments. These findings yield insight in controlled protein assembly and provide principles for assembling microcompartments for biochemical or energy applications as nanoreactors.

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Computational Modeling and Evolutionary Implications of Biochemical Reactions in Bacterial Microcompartments

10.32942/osf.io/352u9 ◽

2021 ◽

Author(s):

Clair A. Huffine ◽

Lucas C. Wheeler ◽

Boswell Wing ◽

Jeffrey Carlyle Cameron

Keyword(s):

Computational Modeling ◽

Substrate Concentration ◽

Reaction Rates ◽

Biochemical Reactions ◽

Ph Gradients ◽

Bacterial Phyla ◽

Bacterial Microcompartments ◽

Oxygen Sensitive ◽

Systematic Understanding ◽

Protein Shell

Bacterial microcompartments (BMCs) are protein-encapsulated compartments found across at least 23 bacterial phyla. BMCs contain a variety of metabolic processes that share the commonality of toxic or volatile intermediates, oxygen-sensitive enzymes and cofactors, or increased substrate concentration for magnified reaction rates. These compartmentalized reactions have been computationally modeled to explore the encapsulated dynamics, ask evolutionary-based questions, and develop a more systematic understanding required for the engineering of novel BMCs. Many crucial aspects of these systems remain unknown or unmeasured, such as substrate permeabilities across the protein shell, feasibility of pH gradients, and transport rates of associated substrates into the cell. This review explores existing BMC models, dominated in the literature by cyanobacterial carboxysomes, and highlights potentially important areas for exploration.

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Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1707009114 ◽

2017 ◽

Vol 114 (36) ◽

pp. 9623-9628 ◽

Cited By ~ 69

Author(s):

Mark Kowarsky ◽

Joan Camunas-Soler ◽

Michael Kertesz ◽

Iwijn De Vlaminck ◽

Winston Koh ◽

...

Keyword(s):

Human Body ◽

Sequence Data ◽

Human Microbiome ◽

Pcr Amplification ◽

The Body ◽

Direct Pcr ◽

Cell Free Dna ◽

Free Dna ◽

Novel Taxa ◽

Circulating Cell Free Dna

Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated.

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