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Directing Biomolecules to Intracellular Microcompartments and Scaffolds

Lawrence Berkeley National Laboratory

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Technology Marketing Summary

Cheryl Kerfeld and James Kinney at Berkeley Lab have identified peptide targeting signals that can direct selected enzymes, metabolites, and other macromolecules to microcompartments or scaffolds used to engineer reactions in cells and non-cellular systems.

To achieve methods of inserting microcompartments into cells and nonliving vesicles to engineer desirable reactions, a targeting signal can be required to bring the enzymes and necessary reaction components to the microcompartment or scaffold. Potential targeting signals identified by Kerfeld and Kinney may serve such a purpose.


The scientists first analyzed the amino acid sequences of enzymes in bacterial microcompartments with diverse functions such as carbon fixation, ethanolamine catabolism, glycyl-radical-based reactions and vitamin-B12-based reactions, among others. The biophysical properties of certain amino acid sequences and an associated linker region were highly conserved among the enzymes from various species and types of microcompartments. These sequences are proposed to bind the conserved hexameric units that, like bathroom tiles, make up the walls of microcompartments. Therefore, these and similar sequences could be attached to desired molecules to direct them to microcompartments or scaffolds.

Microcompartments are protein-based organelles that occur naturally in many bacteria and function as enclosed scaffolds to colocalize enzymes, thereby increasing reaction cascade efficiency. Microcompartment proteins can also be used as two-dimensional molecular layers, i.e., unenclosed scaffolds. Encapsulating reactions within microcompartments protects the surrounding cell from potentially toxic intermediates and conversely protect the enzymes, intermediates, and products from the potentially destabilizing components of the cytoplasm, such as oxygen.

Technologies with microcompartments and scaffolds may be used to improve nonbiological catalysis and introduce new or enhanced metabolic activity to prokaryotes and eukaryotes. The Berkeley Lab peptide sequences provide an essential element in the development of these technologies.


Increases efficiency of catalytic pathways, provides protective microenvironments, enables new combinations and scaffolding of enzymes, compatible with biological and non-biological systems

Applications and Industries

Biomass or biofuel production, carbon dioxide sequestration, nitrogen fixation, bioremediation, protein purification, chemical and pharmaceutical production, other synthetic biology applications

Patents and Patent Applications
ID Number
Title and Abstract
Primary Lab
Application 20130133102
A conserved region of sequence in bacterial microcompartment (BMC) enzymes and proteins was identified. Peptide sequences derived from this conserved region of native BMC proteins and enzymes appear to target the hexameric facets of BMC shell proteins. These peptides were predicted to share general properties of a predicted alpha helical conformation, flanked by poorly conserved segment(s) of primary structure); for each type of encapsulated protein, and for each functionally distinct BMC. These peptides can be used as targeting signals for integrating biomolecules and molecules into bacterial microcompartments or for attaching molecules or biomolecules to native or non-native bacterial microcompartment shell proteins.
Lawrence Berkeley National Laboratory 08/01/2012
Technology Status
Technology IDDevelopment StageAvailabilityPublishedLast Updated
Please reference IB-2785 when inquiring about this technology.Development - Development, bench scale demonstration performedAvailable - Available, patent pending, available for licensing or collaborative research.06/03/201110/21/2013

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To: Shanshan Li<>