Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15

CTX-M15 is one of the most widespread, extended spectrum β-lactamases, a major determinant of antibiotic resistance representing urgent public health threats, among enterobacterial strains infecting humans and animals. Here we describe the selection of binders to CTX-M15 from a combinatorial affibody library displayed on ribosomes. Upon three increasingly selective ribosome display iterations, selected variants were identified by next generation sequencing (NGS). Nine affibody variants with high relative abundance bearing QRP and QLH amino acid motifs at residues 9-11 were produced and characterized in terms of stability, affinity and specificity. All affibodies were correctly folded, with affinities ranging from 0.04 to 2 μM towards CTX-M15, and successfully recognized CTX-M15 in bacterial lysates, culture supernatants and on whole bacteria. It was further demonstrated that the binding of affibody molecules to CTX-M15 modulated the enzyme's kinetic parameters. This work provides an approach using ribosome display coupled to NGS for the rapid generation of protein ligands of interest in diagnostic and research applications.

Simultaneous surface display and cargo loading of encapsulin nanocompartments and their use for rational vaccine design

In the past decades protein nanoparticles have successfully been used for vaccine applications. Their particulate nature and dense repetitive subunit organization makes them perfect carriers for antigen surface display and confers high immunogenicity. Nanoparticles have emerged as excellent candidates for vectorization of biological and immunostimulating molecules. Nanoparticles and biomolecular nanostructures such as ferritins or virus like particles have been used as diagnostic and therapeutic delivery systems, in vaccine development, as nanoreactors, etc. Recently, a new class of bacterial protein compartment has been discovered referred to as encapsulin nanocompartment. These compartments have been used for targeted diagnostics, as therapeutic delivery systems and as nanoreactors. Their biological origin makes them conveniently biocompatible and allows genetic functionalization. The aim of our study was to implement encapsulin nanocompartements for simultaneous epitope surface display and heterologous protein loading for rational vaccine design. For this proof-of-concept-study, we produced Thermotoga maritima encapsulin nanoparticles in E. coli. We demonstrated the ability of simultaneous display in our system by inserting Matrix protein 2 ectodomain (M2e) of influenza A virus at the nanoparticle surface and by packaging of a fluorescent reporter protein (GFP) into the internal cavity. Characterization of the nanoparticles by electronic microscopy confirmed homogenously shaped particles of 24 nm diameter in average. The results further show that engineering of the particle surface improved the loading capacity of the heterologous reporter protein suggesting that surface display may induce a critical elastic deformation resulting in improved stiffness. In Balb/c mice, nanoparticle immunization elicited antibody responses against both the surface epitope and the loaded cargo protein. These results confirm the potential of encapsulin nanocompartments for customized vaccine design and antigen delivery.

Codon harmonization - going beyond the speed limit for protein expression

Codon usage distribution has been soundly used by nature to fine tune protein biogenesis. Alteration of the mRNA structure or sequential scheduling of codons can profoundly affect translation, thus altering protein yield, functionality, solubility, and proper folding. Building on these observations, here, we present an evaluation of different recently designed algorithms of sequence adaptation based on Codon Adaptation Index (CAI) profiling. The first algorithm globally harmonizes synonymous codons in the original sequence in full respect to the heterologous expression host codon usage. The second recodes the sequence in accordance with the native sequence CAI profile. Our data, generated on three model proteins, highlights the importance to consider gene recoding as a parameter itself for recombinant protein expression improvement.