Harnessing the potential of communication-mediating domains for the biocombinatorial synthesis of nonribosomal peptides

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Abstract
The interaction between enzymes of a nonribosomal peptide synthetase (NRPS) complex relies on the interplay of compatible sets of donor and acceptor communication-mediating (COM) domains. Hence, these domains are essential for the formation of a defined biosynthetic template, thereby directing the synthesis of a specific peptide product. Without the selectivity provided by different sets of COM domains, NRPSs should form random biosynthetic templates, which would ultimately lead to combinatorial peptide synthesis. This study aimed to exploit this inherent combinatorial potential of COM domains. Based on sequence alignments between COM domains, the crosstalk between different biosynthetic systems was predicted and experimentally proven. Furthermore, key residues important for maintaining (or preventing) NRPS interaction were identified. Point mutation of one of these key residues within the acceptor COM domain of TycC1 was sufficient to shift its selectivity from the cognate donor COM of TycB3 toward the noncognate donor COM domain of TycB1. Finally, an artificial NRPS complex was constructed, constituted of enzymes derived from three different biosynthetic systems. By virtue of domain fusions, the interactions between all enzymes were established by the same set of COM domains. Because of the abrogated selectivity, this universal communication system was able to simultaneously form two biosynthetic complexes that catalyzed the combinatorial synthesis of different peptide products.