Cell-free protein-based enzyme discovery and protein-ligand interaction study.

Cell-free expression-based screening is sometimes more suitable than cell-based assays for enzyme discovery. The advantage of cell-free systems for expression of toxic, poorly expressed, or insoluble proteins has already been well documented. Cell-free methods can advantageously replace cell-based ones when screening has to be performed on cell lysates prepared from harvested cells, for instance, when dealing with protein-ligand interactions particularly when the latter is hydrophobic. From our experience, cell-free extracts efficient in both transcription and translation can be prepared from potentially any microorganism. Here we present a general method for preparation of cell-free extracts from prokaryotic and eukaryotic cells, selection of the best systems, and optimized conditions for specific protein expression. The method allows to select proteins for their ability to bind a selected target, to identify the inhibitors of such binding, or to identify novel enzymatic activities.

[The prediction of immunogenicity of therapeutic proteins]. / La prédiction de l'immunogénicité des protéines thérapeutiques.

Immunogenicity of therapeutic proteins is a nightmare for industrials because induced antibodies can neutralize the therapeutic activity and provoke autoimmune symptoms. It was believed that sequence humanization would be sufficient to tackle these problems but multiple clinical examples now demonstrate that humanization does not suffice to abrogate immune responses. In order to predict immunogenicity of therapeutic proteins, different approaches have been developed, among which the most relevant ones are based on the evaluation of the response of naïve CD4 T lymphocytes specific for therapeutic proteins. Other approaches also exist or are in development. This review is the state of art in the different technologies that are proposed to predict immunogenicity of therapeutic proteins.

Quantitative analysis of the CD4 T-cell repertoire specific to therapeutic antibodies in healthy donors.

Therapeutic antibodies are generally partially to fully humanized, yet they can show unwanted immunogenicity and lead to antibody response and adverse effects when administered to humans. As immunogenicity relies on a T-cell-dependent mechanism, we have evaluated in vitro the size of the preexisting CD4 T-cell repertoire specific to therapeutic antibodies in healthy donors. Specific CD4 T cells of individuals with different HLA-DR allotypes were amplified by in vitro stimulation and quantified. Well-known immunogenic proteins, KLH and a murine antibody, exhibited a strong in vitro T-cell response characterized by a mean of preexisting T cells >1 cell/10(6) cells. In contrast, the preexisting CD4 T-cell repertoires specific to 2 chimeric, 2 humanized, and 2 fully human antibodies remained generally inferior to this value, confirming the role of species-specific sequences in their shaping. Mean values ranged from 0.01 to 0.3 cell/10(6) cells and varied not necessarily in relationship with the humanization level of the therapeutic antibodies. Relationship with their known immunogenicity is discussed. These results contribute to a better understanding and prediction of immunogenicity of therapeutic antibodies in humans.

Quantification of the preexisting CD4 T-cell repertoire specific for human erythropoietin reveals its immunogenicity potential.

Antibody-mediated pure red cell aplasia is a rare but serious event resulting from the induction of neutralizing erythropoietin (Epo)-specific antibodies provoked by treatment with recombinant Epo. Because of the crucial role of CD4 T cells in humoral response, we have quantified the number of Epo-specific CD4 T cells in the blood of normal donors by in vitro stimulation. An important repertoire of preexisting Epo-specific T cells was observed in almost half of the donors, comparable with that of non-self-proteins. This observation suggests that, at the steady state, endogenous Epo weakly contributes to tolerance induction and may be ignored by the immune system. As a result, circulating Epo-specific CD4 T cells could be prone to be activated by altered batches of Epo, providing them with costimulatory signals. Our data also highlight the relevance of T-cell assays performed with normal donors to evaluate the potential immunogenicity of therapeutic proteins.

A quick in vitro pathway from prokaryotic genomic libraries to enzyme discovery.

Screening of prokaryotic genomes in order to identify enzymes with a desired catalytic activity can be performed in vivo in bacterial cells. We propose a strategy of in vitro expression screening of large prokaryotic genomic libraries based on Escherichia coli cell-free transcription-translation systems. Because cell-based expression may be limited by poor yield or protein misfolding, cell-free expression systems may be advantageous in permitting a more comprehensive screen under conditions optimized for the desired enzyme activity. However, monocistronic messages with an improved leader initiation context are typically used for protein production in vitro. Here, we describe successful use of a Pseudoalteromonas genomic DNA library for in vitro expression of DNA fragments carrying multiple open reading frames (ORFs) in the context of their authentic translation initiation sites and regulatory regions. We show that ORFs located far from the 5' and 3' ends of polycistronic transcripts can be expressed at a sufficient level in an in vitro transcription-translation system in order to allow functional screening. We demonstrate the overall cell-free functional screen strategy with the successful selection of an esterase from Pseudoalteromonas.

In vitro DNA recombination by L-Shuffling during ribosome display affinity maturation of an anti-Fas antibody increases the population of improved variants.

The use of random mutagenesis in concert with protein display technologies to rapidly select high affinity antibody variants is an established methodology. In some cases, DNA recombination has been included in the strategy to enable selection of mutations which act cooperatively to improve antibody function. In this study, the impact of L-Shuffling DNA recombination on the eventual outcome of an in vitro affinity maturation has been experimentally determined. Parallel evolution strategies, with and without a recombination step, were carried out and both methods improved the affinity of an anti-Fas single chain variable fragment (scFv). The recombination step resulted in an increased population of affinity-improved variants. Moreover, the most improved variant, with a 22-fold affinity gain, emerged only from the recombination-based approach. An analysis of mutations preferentially selected in the recombined population demonstrated strong cooperative effects when tested in combination with other mutations but small, or even negative, effects on affinity when tested in isolation. These results underline the ability of combinatorial library approaches to explore very large regions of sequence space to find optimal solutions in antibody evolution studies.

rdlA, a new gene encoding a rhodanese-like protein in Halanaerobium congolense and other thiosulfate-reducing anaerobes.

The recently described anaerobic moderately halophilic bacterium Halanaerobium congolense has been shown to reduce thiosulfate and sulfur-but not sulfate-into sulfide. When cultivated in the presence of thiosulfate as terminal electron acceptor, H. congolense possesses a highly active thiosulfate:cyanide sulfur-transferase activity (rhodanese-like enzyme). A gene library of H. congolense (DSM 11287T) was constructed, and a 3.1-kb Sau3A DNA that encompassed a thiosulfate:cyanide sulfur-transferase-encoding gene was isolated in Escherichia coli. This fragment contains 2 orfs, which were separately subcloned in E. coli. The 900-bp gene encoding the rhodanese-like protein was named rdlA. RdlA differs from other known rhodanese-like proteins by having two potential catalytic sites, one N-terminal and one C-terminal, both harboring a cysteine. The two putative active sites are preceded by a highly-conserved region of unknown function. Closely related genes were also characterized in other thiosulfate-reducing non-sulfate-reducing anaerobes belonging to phylogenetically distant microorganisms, thus suggesting that RdlA is of importance in the mechanism of thiosulfate reduction by numerous members of the domain Bacteria.

Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney.

A strictly anaerobic, slightly halophilic and moderately thermophilic, sporulating rod designated strain DVird3T was isolated from deep-sea hydrothermal vent samples collected at a depth of approximately 800 m on the Atlantic Ocean Ridge. Strain DVird3T possessed a few laterally inserted flagella, had a DNA G + C content of 33.1 mol% and grew optimally at pH 6.6 and at 45 degrees C. Growth was observed at temperatures between 20 and 58 degrees C and at pH values between 5.8 and 8.2. The optimum NaCl concentration for growth was 3% sea salt (30 g l(-1)); no growth was observed in the presence of 15 or 60 g sea salt l(-1). Strain DVird3T is heterotrophic and utilizes some sugars and various single amino acids. Acetate was the main fatty acid detected from carbohydrate fermentation, together with H2 and CO2. Gelatin was used as an energy source. It performed the Stickland reaction. Phylogenetically, strain DVird3T branched with members of cluster XI of the order Clostridiales, with Clostridium halophilum as its closest relative (similarity of 94.6%). On the basis of its phenotypic, genotypic and phylogenetic characteristics, strain DVird3T (= DSM 15212T = CIP 107654T) is proposed as the type strain of a novel species of the genus Clostridium, Clostridium caminithermale sp. nov.