Packaging protein drugs as bacterial inclusion bodies for therapeutic applications
© Villaverde et al.; licensee BioMed Central Ltd. 2012
Received: 30 May 2012
Accepted: 31 May 2012
Published: 11 June 2012
A growing number of insights on the biology of bacterial inclusion bodies (IBs) have revealed intriguing utilities of these protein particles. Since they combine mechanical stability and protein functionality, IBs have been already exploited in biocatalysis and explored for bottom-up topographical modification in tissue engineering. Being fully biocompatible and with tuneable bio-physical properties, IBs are currently emerging as agents for protein delivery into mammalian cells in protein-replacement cell therapies. So far, IBs formed by chaperones (heat shock protein 70, Hsp70), enzymes (catalase and dihydrofolate reductase), grow factors (leukemia inhibitory factor, LIF) and structural proteins (the cytoskeleton keratin 14) have been shown to rescue exposed cells from a spectrum of stresses and restore cell functions in absence of cytotoxicity. The natural penetrability of IBs into mammalian cells (reaching both cytoplasm and nucleus) empowers them as an unexpected platform for the controlled delivery of essentially any therapeutic polypeptide. Production of protein drugs by biopharma has been traditionally challenged by IB formation. However, a time might have arrived in which recombinant bacteria are to be engineered for the controlled packaging of therapeutic proteins as nanoparticulate materials (nanopills), for their extra- or intra-cellular release in medicine and cosmetics.
Since the full acknowledgment of bacterial inclusion bodies (IBs) as formed by functional polypeptides[1, 2], enzyme-based IBs have been exploited as naturally immobilized catalysts with high operational stability[3, 4]. Pull-down peptides, incorporated to target proteins as end-terminal fusions, favor the deposition of properly folded polypeptides in Escherichia coli as functional IBs[5–7]. This is especially relevant as these tags can drive protein deposition even under production conditions that favor protein folding (eg. suboptimal growth temperature), then enriching IBs with biologically active polypeptides[1, 8–10].
Being mechanically stable, purified IBs have been recently observed as promising nanoparticulate materials[3, 11–16], whose biological and nanoscale properties can be modulated by the appropriate selection of the E. coli host strain and of production/handing conditions. In particular, IBs have been explored as agents for topographical modification in tissue engineering[11, 17–19]. Being bio-adhesive, they favor mammalian cell attachment to IB-decorated surfaces but also offer convenient mechanical effectors within the mammalian cell sensing range that stimulate ERK-mediated cell proliferation. No signs of toxicity or cell apoptosis have been ever observed in these studies. Previously reported toxicity on mammalian cells upon exposure to high amounts of IBs could be linked to obsolete purification protocols leaving IBs contaminated with living bacterial cells or toxic debris. Interestingly, in bottom-up IB decoration, the mammalian cell membrane is in intimate contact with IBs and cell sensing agents (filopodia/lamelipodia) are stimulated in presence of substrate IBs.
Taken together, the relatively cost-efficient production/downstream of IBs in E. coli, their biological activity, the tunability of their biological and nano-mechanical properties, their biocompatibility in cell interfaces[18, 19, 21], the release of functional IB proteins in aqueous conditions[8, 22] and the apparent avidity of IBs for mammalian cell membranes[11, 17] drives to the intriguing question about if these protein particles could deliver embedded therapeutic proteins into mammalian cells. If so, these bacterially produced nanoparticles could act as nanopills, that is, nanosized clusters of functional and bioavailable protein drugs. Recombinant E. coli cells would then turn into convenient factories for the tailored packaging of protein drugs as nanopills, since essentially any protein (with or without therapeutic potential) can be produced as bacterial IBs. The same limitations defining the suitability of soluble proteins produced in E. coli as biopharmaceuticals (eg. biological activity depending on post-translational modifications, missing in bacteria, or proteolytic instability) would be relevant to bacterial nanopills.
The precise mechanisms by which IBs get naturally embedded and cross both cellular and nuclear membranes should be investigated, but we might anticipate that hydrophobic, solvent-exposed protein patches in IBs might have a role in there, as it occurs with cell penetrating peptides of common use for intracellular drug delivery. Also, how functional proteins are released from IBs once in the cytoplasmic and nuclear compartments deserves additional analysis, to set a basis for further improvement of IB properties through protein or process engineering. A recent model proposing a cotton-like structure for bacterial IBs figures out IBs as mainly composed by releasable soluble protein, entrapped into the gaps of a more stable scaffold.
In this regard, and being natural products, bacterial IBs are not homogeneous in their compositional analysis. IBs are in general almost exclusively formed by the target protein with little contamination of other proteins[12, 28, 29]. There are also strong indications that upon co-expression of different aggregation-prone proteins these species do not co-aggregate, but deposit into distinguishable IBs[30, 31]. However, truncated versions of the target protein[32, 33], other plasmid-encoded proteins[34, 35], but also defined host cell proteins[34, 36] including folding assistant proteins[36–39] may get entrapped within or associated to bacterial IBs. Mostly, the majority of host cell and plasmid derived contaminants (e.g. plasmid DNA, lipids, membrane components) in IB preparations reflect unspecific adsorption and co-precipitation of cell debris during IB purification. Most of these contaminants can be removed by thorough purification procedures[40–42], and new protocols for IB purification have been recently communicated that permit to obtain these particles relatively free from contaminating cell debris, and specially from living bacteria escaping from cell lysis[41, 42].
Bacterial IBs show a great and unexpected potential as cost-effective protein delivery agents. Available genetic and process tools permit the tailoring of relevant IB properties and prompt an immediate investigation of the new opportunities offered by IBs as nanopills, for advanced therapies in translational and innovative medicines.
We appreciate the financial support received for the development of therapeutic inclusion bodies and of the Nanopill concept from MICINN (BFU2010-17450), AGAUR (2009SGR-108) and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain. A. Villaverde has been granted with an ICREA ACADEMIA award (from ICREA, Catalonia, Spain) and EGF is supported by the Programa Personal de Técnico de Apoyo (Modalidad Infraestructuras científco-tecnológicas, MICINN). JSF is a PIF fellowship holder from UAB, Spain.
- Jevsevar S, Gaberc-Porekar V, Fonda I, Podobnik B, Grdadolnik J, Menart V: Production of nonclassical inclusion bodies from which correctly folded protein can be extracted. Biotechnol Prog. 2005, 21: 632-639.View ArticleGoogle Scholar
- Garcia-Fruitos E, Gonzalez-Montalban N, Morell M, Vera A, Ferraz RM, Aris A, et al: Aggregation as bacterial inclusion bodies does not imply inactivation of enzymes and fluorescent proteins. Microb Cell Fact. 2005, 4: 27-View ArticleGoogle Scholar
- Garcia-Fruitos E, Vazquez E, Diez-Gil C, Corchero JL, Seras-Franzoso J, Ratera I, et al: Bacterial inclusion bodies: making gold from waste. Trends Biotechnol. 2012, 30: 65-70.View ArticleGoogle Scholar
- Garcia-Fruitos E, Villaverde A: Friendly production of bacterial inclusion bodies. Korean J Chem Eng. 2010, 27: 385-389.View ArticleGoogle Scholar
- Nahalka J, Nidetzky B: Fusion to a pull-down domain: a novel approach of producingTrigonopsis variabilisD-amino acid oxidase as insoluble enzyme aggregates. Biotechnol Bioeng. 2007, 97: 454-461.View ArticleGoogle Scholar
- Wu W, Xing L, Zhou B, Lin Z: Active protein aggregates induced by terminally attached self-assembling peptide ELK16 inEscherichia coli. Microb Cell Fact. 2011, 10: 9-View ArticleGoogle Scholar
- Zhou B, Xing L, Wu W, Zhang XE, Lin Z: Small surfactant-like peptides can drive soluble proteins into active aggregates. Microb Cell Fact. 2012, 11: 10-View ArticleGoogle Scholar
- Peternel S, Grdadolnik J, Gaberc-Porekar V, Komel R: Engineering inclusion bodies for non denaturing extraction of functional proteins. Microb Cell Fact. 2008, 7: 34-View ArticleGoogle Scholar
- Vera A, Gonzalez-Montalban N, Aris A, Villaverde A: The conformational quality of insoluble recombinant proteins is enhanced at low growth temperatures. Biotechnol Bioeng. 2007, 96: 1101-1106.View ArticleGoogle Scholar
- Gonzalez-Montalban N, Garcia-Fruitos E, Villaverde A: Recombinant protein solubility-does more mean better?. Nat Biotechnol. 2007, 25: 718-720.View ArticleGoogle Scholar
- García-Fruitós E, Rodríguez-Carmona E, Díez-Gil C, Ferraz RM, Vázquez E, Corchero JL, et al: Surface Cell Growth Engineering Assisted by a Novel Bacterial Nanomaterial. Advanced Materials. 2009, 21: 4249-4253.View ArticleGoogle Scholar
- Mitraki A: Protein aggregation from inclusion bodies to amyloid and biomaterials. Adv Protein Chem Struct Biol. 2010, 79: 89-125.View ArticleGoogle Scholar
- Peternel S, Komel R: Active Protein Aggregates Produced inEscherichia coli. Int J Mol Sci. 2011, 12: 8275-8287.View ArticleGoogle Scholar
- Rodriguez-Carmona E, Villaverde A: Nanostructured bacterial materials for innovative medicines. Trends Microbiol. 2010, 18: 423-430.View ArticleGoogle Scholar
- Villaverde A: Nanotechnology, bionanotechnology and microbial cell factories. Microb Cell Fact. 2010, 9: 53-View ArticleGoogle Scholar
- Vazquez E, Villaverde A: Engineering building blocks for self-assembling protein nanoparticles. Microb Cell Fact. 2010, 9: 101-View ArticleGoogle Scholar
- Seras-Franzoso J, Diez-Gil C, Vazquez E, Garcia-Fruitos E, Cubarsi R, Ratera I, et al: Bioadhesiveness and efficient mechanotransduction stimuli synergistically provided by bacterial inclusion bodies as scaffolds for tissue engineering. Nanomedicine (Lond). 2012, 7: 79-93.View ArticleGoogle Scholar
- Garcia-Fruitos E, Seras-Franzoso J, Vazquez E, Villaverde A: Tunable geometry of bacterial inclusion bodies as substrate materials for tissue engineering. Nanotechnology. 2010, 21: 205101-View ArticleGoogle Scholar
- Diez-Gil C, Krabbenborg S, Garcia-Fruitos E, Vazquez E, Rodriguez-Carmona E, Ratera I, et al: The nanoscale properties of bacterial inclusion bodies and their effect on mammalian cell proliferation. Biomaterials. 2010, 31: 5805-5812.View ArticleGoogle Scholar
- Gonzalez-Montalban N, Villaverde A, Aris A: Amyloid-linked cellular toxicity triggered by bacterial inclusion bodies. Biochem Biophys Res Commun. 2007, 355: 637-642.View ArticleGoogle Scholar
- Gonzalez P, Peluffo H, Acarin L, Villaverde A, Gonzalez B, Castellano B: Interleukin-10 overexpression does not synergize with the neuroprotective action of RGD-containing vectors after postnatal brain excitotoxicity but modulates the main inflammatory cell responses. J Neurosci Res. 2012, 90: 143-159.View ArticleGoogle Scholar
- Garcia-Fruitos E, Aris A, Villaverde A: Localization of functional polypeptides in bacterial inclusion bodies. Appl Environ Microbiol. 2007, 73: 289-294.View ArticleGoogle Scholar
- Villaverde A, Carrio MM: Protein aggregation in recombinant bacteria: biological role of inclusion bodies. Biotechnol Lett. 2003, 25: 1385-1395.View ArticleGoogle Scholar
- García-Fruitós E, Vazquez E, Corchero JL, Villaverde A: Use of inclusion bodies as therapeutic agents. [WO2010131117A1]. 18-11-2010Google Scholar
- Vazquez E, Corchero JL, Burgueno JF, Seras-Franzoso J, Kosoy A, Bosser R, et al: Functional inclusion bodies produced in bacteria as naturally occurring nanopills for advanced cell therapies. Adv Mater. 2012, 24: 1742-1747.View ArticleGoogle Scholar
- Liovic M, Ozir M, Bedina ZA, Peternel S, Komel R, Zupancic T: Inclusion bodies as potential vehicles for recombinant protein delivery into epithelial cells. Microb Cell Fact. 2012, 11: 67-View ArticleGoogle Scholar
- Ferrer-Miralles N, Vazquez E, Villaverde A: Membrane-active peptides for non-viral gene therapy: making the safest easier. Trends Biotechnol. 2008, 26: 267-275.View ArticleGoogle Scholar
- Garcia-Fruitos E, Sabate R, de Groot NS, Villaverde A, Ventura S: Biological role of bacterial inclusion bodies: a model for amyloid aggregation. FEBS J. 2011, 278: 2419-2427.View ArticleGoogle Scholar
- Carrio M, Gonzalez-Montalban N, Vera A, Villaverde A, Ventura S: Amyloid-like properties of bacterial inclusion bodies. J Mol Biol. 2005, 347: 1025-1037.View ArticleGoogle Scholar
- Speed MA, Wang DI, King J: Specific aggregation of partially folded polypeptide chains: the molecular basis of inclusion body composition. Nat Biotechnol. 1996, 14: 1283-1287.View ArticleGoogle Scholar
- Morell M, Bravo R, Espargaro A, Sisquella X, Aviles FX, Fernandez-Busquets X, et al: Inclusion bodies: specificity in their aggregation process and amyloid-like structure. Biochim Biophys Acta. 2008, 1783: 1815-1825.View ArticleGoogle Scholar
- Rinas U, Boone TC, Bailey JE: Characterization of inclusion bodies in recombinantEscherichia coliproducing high levels of porcine somatotropin. J Biotechnol. 1993, 28: 313-320.View ArticleGoogle Scholar
- Rinas U, Bailey JE: Protein compositional analysis of inclusion bodies produced in recombinantEscherichia coli. Appl Microbiol Biotechnol. 1992, 37: 609-614.Google Scholar
- Hart RA, Rinas U, Bailey JE: Protein composition ofVitreoscillahemoglobin inclusion bodies produced inEscherichia coli. J Biol Chem. 1990, 265: 12728-12733.Google Scholar
- Neubauer A, Soini J, Bollok M, Zenker M, Sandqvist J, Myllyharju J, et al: Fermentation process for tetrameric human collagen prolyl 4-hydroxylase inEscherichia coli: Improvement by gene optimisation of the PDI/beta subunit and repeated addition of the inducer anhydrotetracycline. J Biotechnol. 2007, 128: 308-321.View ArticleGoogle Scholar
- Rinas U, Hoffmann F, Betiku E, Estape D, Marten S: Inclusion body anatomy and functioning of chaperone-mediated in vivo inclusion body disassembly during high-level recombinant protein production inEscherichia coli. J Biotechnol. 2007, 127: 244-257.View ArticleGoogle Scholar
- Allen SP, Polazzi JO, Gierse JK, Easton AM: Two novel heat shock genes encoding proteins produced in response to heterologous protein expression inEscherichia coli. J Bacteriol. 1992, 174: 6938-6947.Google Scholar
- Carrio MM, Villaverde A: Construction and deconstruction of bacterial inclusion bodies. J Biotechnol. 2002, 96: 3-12.View ArticleGoogle Scholar
- Carrio MM, Villaverde A: Localization of chaperones DnaK and GroEL in bacterial inclusion bodies. J Bacteriol. 2005, 187: 3599-3601.View ArticleGoogle Scholar
- Estape D, Rinas U: Folding kinetics of the all-beta-sheet protein human basic fibroblast growth factor, a structural homolog of interleukin-1beta. J Biol Chem. 1999, 274: 34083-34088.View ArticleGoogle Scholar
- Peternel S, Komel R: Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells. Microb Cell Fact. 2010, 9: 66-View ArticleGoogle Scholar
- Rodriguez-Carmona E, Cano-Garrido O, Seras-Franzoso J, Villaverde A, Garcia-Fruitos E: Isolation of cell-free bacterial inclusion bodies. Microb Cell Fact. 2010, 9: 71-View ArticleGoogle Scholar
- Maji SK, Perrin MH, Sawaya MR, Jessberger S, Vadodaria K, Rissman RA, et al: Functional amyloids as natural storage of peptide hormones in pituitary secretory granules. Science. 2009, 325: 328-332.View ArticleGoogle Scholar
- Maji SK, Schubert D, Rivier C, Lee S, Rivier JE, Riek R: Amyloid as a depot for the formulation of long-acting drugs. PLoS Biol. 2008, 6: e17-View ArticleGoogle Scholar
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