Innate and engineered attributes of bacterial microcompartments for applications in bio-materials science

Sinha, Sharmistha; Rose, S M; Radhakrishnan, Aarcha

doi:10.1039/d3tb00098b

Cited by 4 publications

(3 citation statements)

References 107 publications

(148 reference statements)

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“…These inquiries are likely to uncover novel mechanisms within basic prokaryotic cellular biology, including extending knowledge related to the sorting of proteins within bacterial cells. In addition, the potential to engineer other protein toxins or molecules for targeted delivery into the MFM lumen and PB could be of value to the biotechnology industry, including applications in drug delivery, as has been proposed for encapsulins and microcompartment organelles [37][38][39][40][41][42][43][44]. We hope these observations stimulate further interest and research into the structural organization and biogenesis of Bti's PB.…”

Section: Discussionmentioning

confidence: 88%

The Parasporal Body of Bacillus thuringiensis subsp. israelensis: A Unique Phage Capsid-Associated Prokaryotic Insecticidal Organelle

Rudd,

Miranda,

Curtis

et al. 2023

Biology

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The three most important commercial bacterial insecticides are all derived from subspecies of Bacillus thuringiensis (Bt). Specifically, Bt subsp. kurstaki (Btk) and Bt subsp. aizawai (Bta) are used to control larval lepidopteran pests. The third, Bt subsp. israelensis (Bti), is primarily used to control mosquito and blackfly larvae. All three subspecies produce a parasporal body (PB) during sporulation. The PB is composed of insecticidal proteins that damage the midgut epithelium, initiating a complex process that results in the death of the insect. Among these three subspecies of Bt, Bti is unique as it produces the most complex PB consisting of three compartments. Each compartment is bound by a multilaminar fibrous matrix (MFM). Two compartments contain one protein each, Cry11Aa1 and Cyt1Aa1, while the third contains two, Cry4Aa1/Cry4Ba1. Each compartment is packaged independently before coalescing into the mature spherical PB held together by additional layers of the MFM. This distinctive packaging process is unparalleled among known bacterial organelles, although the underlying molecular biology is yet to be determined. Here, we present structural and molecular evidence that the MFM has a hexagonal pattern to which Bti proteins Bt152 and Bt075 bind. Bt152 binds to a defined spot on the MFM during the development of each compartment, yet its function remains unknown. Bt075 appears to be derived from a bacteriophage major capsid protein (MCP), and though its sequence has markedly diverged, it shares striking 3-D structural similarity to the Escherichia coli phage HK97 Head 1 capsid protein. Both proteins are encoded on Bti’s pBtoxis plasmid. Additionally, we have also identified a six-amino acid motif that appears to be part of a novel molecular process responsible for targeting the Cry and Cyt proteins to their cytoplasmic compartments. This paper describes several previously unknown features of the Bti organelle, representing a first step to understanding the biology of a unique process of sorting and packaging of proteins into PBs. The insights from this research suggest a potential for future applications in nanotechnology.

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Section: Discussionmentioning

confidence: 88%

The Parasporal Body of Bacillus thuringiensis subsp. israelensis: A Unique Phage Capsid-Associated Prokaryotic Insecticidal Organelle

Rudd,

Miranda,

Curtis

et al. 2023

Biology

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“…6,7 For all of these reasons, BMC shell are emerging as engineering platforms for abiotic and biotic catalysis. [8][9][10][11] A crucial limitation for engineering new catalytic pathways into BMC shell are whether reactants and products permeate across the shell. Natural BMCs are permeable to a wide range of metabolites, such as bicarbonate and Calvin-Benson-Bassham cycle intermediates to facilitate carbon fixation in cyanobacterial carboxysomes, 12 or reactants and products for propanediol, 13 ethanomine, 14 frucose or rhamnose 15 synthesis.…”

Section: Introductionmentioning

confidence: 99%

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Raza,

Sarkar,

Chan

et al. 2024

Preprint

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Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles, typically trimers, hexamers, or pentamers, and these tiles assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We use molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceum model BMC. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

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“…Enzyme compartmentalization increases the rate of catabolism which increases fitness . BMC shells also serve to protect encapsulated enzymes from deleterious metabolites, such as O 2 for oxygen-sensitive enzymes. , For all of these reasons, BMC shells are emerging as engineering platforms for abiotic and biotic catalysis. − …”

Section: Introductionmentioning

confidence: 99%

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Raza,

Sarkar,

Chan

et al. 2024

ACS Omega

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Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We used molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed the overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceum model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

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Innate and engineered attributes of bacterial microcompartments for applications in bio-materials science

Abstract: Bacterial Microcompartments (BMCs) are sophisticated all protein bionanoreactors widely spreaded in bacterial phyla. BMCs entrap diverse metabolic reactions, which assist bacterial survivability in normal (by fixing carbon dioxide) and energy...

Cited by 4 publications

References 107 publications

The Parasporal Body of Bacillus thuringiensis subsp. israelensis: A Unique Phage Capsid-Associated Prokaryotic Insecticidal Organelle

The Parasporal Body of Bacillus thuringiensis subsp. israelensis: A Unique Phage Capsid-Associated Prokaryotic Insecticidal Organelle

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

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