Engineering Bacterial Microcompartment Shells: Chimeric Shell Proteins and Chimeric Carboxysome Shells

2014 ◽  
Vol 4 (4) ◽  
pp. 444-453 ◽  
Author(s):  
Fei Cai ◽  
Markus Sutter ◽  
Susan L. Bernstein ◽  
James N. Kinney ◽  
Cheryl A. Kerfeld
Keyword(s):  
Bacterial Microcompartment ◽  
Shell Proteins

scholarly journals Functionalization of Bacterial Microcompartment Shell Proteins With Covalently Attached Heme

2020 ◽  
Vol 7 ◽  
Author(s):  
Jingcheng Huang ◽  
Bryan H. Ferlez ◽  
Eric J. Young ◽  
Cheryl A. Kerfeld ◽  
David M. Kramer ◽  
...  
Keyword(s):  
Bacterial Microcompartment ◽  
Shell Proteins

Redox Characterization of Electrode-Immobilized Bacterial Microcompartment Shell Proteins Engineered To Bind Metal Centers

2019 ◽  
Vol 3 (1) ◽  
pp. 685-692 ◽  
Author(s):  
Jefferson S. Plegaria ◽  
Matthew D. Yates ◽  
Sarah M. Glaven ◽  
Cheryl A. Kerfeld
Keyword(s):  
Metal Centers ◽  
Bacterial Microcompartment ◽  
Shell Proteins

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

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

scholarly journals Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization of Propionibacterium freudenreichii

2021 ◽  
Vol 12 ◽  
Author(s):  
Alexander Dank ◽  
Zhe Zeng ◽  
Sjef Boeren ◽  
Richard A. Notebaart ◽  
Eddy J. Smid ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Probiotic Bacterium ◽  
Vitamin B ◽  
Propionibacterium Freudenreichii ◽  
Human Gut ◽  
Bacterial Microcompartment ◽  
Gut Colonization ◽  
Transmission Electron ◽  
Shell Proteins ◽  
Repair Mechanisms

Bacterial microcompartments (BMCs) are proteinaceous prokaryotic organelles that enable the utilization of substrates such as 1,2-propanediol and ethanolamine. BMCs are mostly linked to the survival of particular pathogenic bacteria by providing a growth advantage through utilization of 1,2-propanediol and ethanolamine which are abundantly present in the human gut. Although a 1,2-propanediol utilization cluster was found in the probiotic bacterium Propionibacterium freudenreichii, BMC-mediated metabolism of 1,2-propanediol has not been demonstrated experimentally in P. freudenreichii. In this study we show that P. freudenreichii DSM 20271 metabolizes 1,2-propanediol in anaerobic conditions to propionate and 1-propanol. Furthermore, 1,2-propanediol induced the formation of BMCs, which were visualized by transmission electron microscopy and resembled BMCs found in other bacteria. Proteomic analysis of 1,2-propanediol grown cells compared to L-lactate grown cells showed significant upregulation of proteins involved in propanediol-utilization (pdu-cluster), DNA repair mechanisms and BMC shell proteins while proteins involved in oxidative phosphorylation were down-regulated. 1,2-Propanediol utilizing cells actively produced vitamin B12 (cobalamin) in similar amounts as cells growing on L-lactate. The ability to metabolize 1,2-propanediol may have implications for human gut colonization and modulation, and can potentially aid in delivering propionate and vitamin B12in situ.

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

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.

scholarly journals Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly

2021 ◽  
Vol 433 (2) ◽  
pp. 166721
Author(s):  
Nolan W. Kennedy ◽  
Svetlana P. Ikonomova ◽  
Marilyn Slininger Lee ◽  
Henry W. Raeder ◽  
Danielle Tullman-Ercek
Keyword(s):  
Bacterial Microcompartment ◽  
Self Assembling ◽  
Shell Proteins

scholarly journals Many-molecule encapsulation by an icosahedral shell

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Jason D Perlmutter ◽  
Farzaneh Mohajerani ◽  
Michael F Hagan
Keyword(s):  
Carbonic Anhydrase ◽  
Protein Interactions ◽  
Carbon Fixation ◽  
The Other ◽  
Control Parameters ◽  
Bisphosphate Carboxylase ◽  
Bacterial Microcompartment ◽  
Shell Proteins ◽  
Assembly Pathways

We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants.

scholarly journals A Survey of Bacterial Microcompartment Distribution in the Human Microbiome

2021 ◽  
Vol 12 ◽  
Author(s):  
Kunica Asija ◽  
Markus Sutter ◽  
Cheryl A. Kerfeld
Keyword(s):  
Sequence Data ◽  
Human Microbiome ◽  
Metabolic Potential ◽  
Bacterial Phyla ◽  
Bacterial Microcompartments ◽  
Bacterial Microcompartment ◽  
Different Types ◽  
Shell Proteins ◽  
Enzymatic Pathways ◽  
Protein Shell

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.

scholarly journals Anaerobic growth of Listeria monocytogenes on rhamnose is stimulated by Vitamin B12 and bacterial microcompartment dependent 1,2-propanediol utilization

2021 ◽  
Author(s):  
Zhe Zeng ◽  
Siming Li ◽  
Sjef Boeren ◽  
Eddy J. Smid ◽  
Richard A. Notebaart ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Vitamin B12 ◽  
Anaerobic Growth ◽  
Physiological Effects ◽  
Human Intestine ◽  
Human Pathogens ◽  
Bacterial Microcompartment ◽  
Food Borne ◽  
Transmission Electron ◽  
Shell Proteins

AbstractThe food-borne pathogen Listeria monocytogenes is able to form proteinaceous organelles called bacterial microcompartments (BMCs) that optimize the utilization of substrates, such as 1,2-propanediol, and confer an anaerobic growth advantage. Rhamnose is a deoxyhexose sugar abundant in a range of environments including the human intestine, and can be degraded in anaerobic conditions into 1,2-propanediol, next to acetate and lactate. Rhamnose-derived 1,2-propanediol has been found to link with BMCs in a limited number of commensal human colonic species and some human pathogens such as Salmonella enterica, but the involvement of BMCs in rhamnose metabolism and potential physiological effects on L. monocytogenes are still unknown. In this study, we firstly test the effect of rhamnose uptake and utilization on anaerobic growth of L. monocytogenes EGDe without and with added vitamin B12, followed by metabolic analysis. We unveil that the vitamin B12-dependent activation of pdu stimulates metabolism and anaerobic growth of L. monocytogenes EGDe on rhamnose via 1,2-propanediol degradation into 1-propanol and propionate. Transmission electron microscopy of pdu-induced cells shows that BMCs are formed and additional proteomics experiments confirm expression of pdu BMC shell proteins and enzymes. Finally, we discuss physiological effects and energy efficiency of L. monocytogenes pdu BMC-driven anaerobic rhamnose metabolism and impact on competitive fitness in environments such as the human intestine.

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