Recombinant expression of insoluble enzymes in Escherichia coli: a systematic review of experimental design and its manufacturing implications

Recombinant enzyme expression in Escherichia coli is one of the most popular methods to produce bulk concentrations of protein product. However, this method is often limited by the inadvertent formation of inclusion bodies. Our analysis systematically reviews literature from 2010 to 2021 and details the methods and strategies researchers have utilized for expression of difficult to express (DtE), industrially relevant recombinant enzymes in E. coli expression strains. Our review identifies an absence of a coherent strategy with disparate practices being used to promote solubility. We discuss the potential to approach recombinant expression systematically, with the aid of modern bioinformatics, modelling, and ‘omics’ based systems-level analysis techniques to provide a structured, holistic approach. Our analysis also identifies potential gaps in the methods used to report metadata in publications and the impact on the reproducibility and growth of the research in this field.

Asymmetric bifunctional protein nanoparticles through redesign of self-assembly

Engineering oligomeric protein self-assembly is an attractive approach to fabricate nanostructures with well-defined geometries, stoichiometry and functions. The homodecamer Brucella Lumazine Synthase (BLS) is a highly stable and immunogenic protein nanoparticle (PNP). Here, we engineered the BLS protein scaffold to display two functions in spatially opposite regions of its structure yielding a Janus-like nanoparticle. An in silico analysis of the BLS head-to-head dimer of homopentamers shows major inter-pentameric interactions located in the equatorial interface. Based on this analysis, two BLS protomer variants were designed to interrupt pentamer self-dimerization and promote heteropentameric dimers. This strategy enabled us to generate a decameric particle with two distinct sides formed by two independent pentamers. The versatility of this new self-assembly nanofabrication strategy is illustrated with two example applications. First, a bifunctional BLS bearing Alexa Fluor 488 fluorophores on one side and sialic acid binding domains on the other side was used for labelling murine and human cells and analyzed by flow cytometry and confocal microscopy. Second, multichromophoric FRET nanoparticles were fabricated and characterized at the single molecule level, showing discrete energy transfer events. The engineered BLS variants constitute a general platform for displaying two functions in a controlled manner within the same PNP with potential applications in various areas such as biomedicine, biotechnology and nanotechnology.

Recent advances in riboflavin biosynthesis

Riboflavin is biosynthesized from GTP and ribulose 5-phosphate. Whereas the early reactions conducing to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate show significant taxonomic variation, the subsequent reaction steps are universal in all taxonomic kingdoms. With the exception of a hitherto elusive phosphatase, all enzymes of the pathway have been characterized in some detail at the structural and mechanistic level. Some of the pathway enzymes (GTP cycloyhdrolase II, 3,4-dihydroxy-2-butanone 4-phosphate synthase, riboflavin synthase) have exceptionally complex reaction mechanisms. The commercial production of the vitamin is now entirely based on highly productive fermentation processes. Due to their absence in animals, the pathway enzymes are potential targets for the development of novel anti-infective drugs.

Conversion of a dodecahedral protein capsid into pentamers via minimal point mutations

Protein self-assembly relies upon the formation of stabilizing noncovalent interactions across subunit interfaces. Identifying the determinants of self-assembly is crucial for understanding structure-function relationships in symmetric protein complexes and for engineering responsive nanoscale architectures for applications in medicine and biotechnology. Lumazine synthases (LS's) comprise a protein family that forms diverse quaternary structures, including pentamers and 60-subunit dodecahedral capsids. To improve our understanding of the basis for this difference in assembly, we attempted to convert the capsid-forming LS from Aquifex aeolicus (AaLS) into pentamers through a small number of rationally designed amino acid substitutions. Our mutations targeted side chains at ionic (R40), hydrogen bonding (H41), and hydrophobic (L121 and I125) interaction sites along the interfaces between pentamers. We found that substitutions at two or three of these positions could reliably generate pentameric variants of AaLS. Biophysical characterization indicates that this quaternary structure change is not accompanied by substantial changes in secondary or tertiary structure. Interestingly, previous homology-based studies of the assembly determinants in LS's had identified only one of these four positions. The ability to control assembly state in protein capsids such as AaLS could aid efforts in the development of new systems for drug delivery, biocatalysis, or materials synthesis.