Despite efforts to develop concepts for efficient antibody fragment (Fab) production in Escherichia coli (E. coli) and the high degree of similarity within this protein class, a generic platform technology is still not available. Indeed, feasible production of new Fab candidates remains challenging. In this study, a setup that enables direct characterization of host cell response to Fab expression by utilizing genome‐integrated (GI) systems is established. Among the multitude of factors that influence Fab expression, the variable domain, the translocation mechanism, the host strain, as well as the copy number of the gene of interest (GOI) are varied. The resulting 32 production clones are characterized in carbon‐limited microbioreactor cultivations with yields of 0–7.4 mg Fab per gram of cell dry mass. Antigen‐binding region variations have the greatest effect on Fab yield. In most cases, the E. coli HMS174(DE3) strain performs better than the BL21(DE3) strain. Translocation mechanism variations mainly influence leader peptide cleavage efficiency. Plasmid‐free systems, with a single copy of the GOI integrated into the chromosome, reach Fab yields in the range of 80–300% of plasmid‐based counterparts. Consequently, the GI Fab production clones could greatly facilitate direct analyses of systems response to different impact factors under varying production conditions.
Antibody fragments
such as Fab’s require the formation of
disulfide bonds to achieve a proper folding state. During their recombinant,
periplasmic expression in
Escherichia coli
, oxidative folding is mediated by the DsbA/DsbB system in concert
with ubiquinone. Thereby, overexpression of Fab’s is linked
to the respiratory chain, which is not only immensely important for
the cell’s energy household but also known as a major source
of reactive oxygen species. However, the effects of an increased oxidative
folding demand and the consequently required electron flux via ubiquinone
on the host cell have not been characterized so far. Here, we show
that Fab expression in
E. coli
BL21(DE3)
interfered with the intracellular redox balance, thereby negatively
impacting host cell performance. Production of four different model
Fab’s in lab-scale fed-batch cultivations led to increased
oxygen consumption rates and strong cell lysis. An RNA sequencing
analysis revealed transcription activation of the oxidative stress-responsive
soxS
gene in the Fab-producing strains. We attributed this
to the accumulation of intracellular superoxide, which was measured
using flow cytometry. An exogenously supplemented ubiquinone analogue
improved Fab yields up to 82%, indicating that partitioning of the
quinone pool between aerobic respiration and oxidative folding limited
ubiquinone availability and hence disulfide bond formation capacity.
Combined, our results provide a more in-depth understanding of the
profound effects that periplasmic Fab expression and in particular
disulfide bond formation has on the host cell. Thereby, we show new
possibilities to elaborate cell engineering and process strategies
for improved host cell fitness and process outcome.
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