Folding reporters are proteins with easily identifiable phenotypes, such as antibiotic resistance, whose folding and function is compromised when
fused to poorly folding proteins or random open reading frames. We have developed a strategy where, by using TEM-1 β-lactamase (the enzyme
conferring ampicillin resistance) on a genomic scale, we can select collections of correctly folded protein domains from the coding portion of the
DNA of any intronless genome. The protein fragments obtained by this approach, the so called "domainome", will be well expressed and soluble,
making them suitable for structural/functional studies.
By cloning and displaying the "domainome" directly in a phage display system, we have showed that it is possible to select specific protein
domains with the desired binding properties (e.g., to other proteins or to antibodies), thus providing essential experimental information for gene
annotation or antigen identification.
The identification of the most enriched clones in a selected polyclonal population can be achieved by using novel next-generation sequencing
technologies (NGS). For these reasons, we introduce deep sequencing analysis of the library itself and the selection outputs to provide complete
information on diversity, abundance and precise mapping of each of the selected fragment. The protocols presented here show the key steps for
library construction, characterization, and validation.
