Prenylation: A Critical Step for Biomanufacturing of Prenylated Aromatic Natural Products

Abstract

Prenylated aromatic natural products (PANPs) have received much attention due to their biomedical benefits for human health. The prenylation of aromatic natural products (ANPs), which is mainly catalyzed by aromatic prenyltransferases (aPTs), contributes significantly to their structural and functional diversity by providing higher lipophilicity and enhanced bioactivity. aPTs are widely distributed in bacteria, fungi, animals, and plants and play a key role in the regiospecific prenylation of ANPs. Recent studies have greatly advanced our understanding of the characteristics and application of aPTs. In this review, we comment on research progress regarding sources, evolutionary relationships, structural features, reaction mechanism, engineering modification, and application of aPTs. Particular emphasis is also placed on recent advances, challenges, and prospects about applications of aPTs in microbial cell factories for producing PANPs. Generally, this review could provide guidance for using aPTs as robust biocatalytic tools to produce various PANPs with high efficiency.

A Gatekeeper Residue Controls Aromatic Acceptor Specificity of the PHB-Type UbiA Prenyltransferases

“…31 Identification of the gatekeeper residues in DMATS-type PTs to control the size of the prenyl donor largely expanded the biocatalytic tools. 12 Herein, by mutating the identified gatekeeper residue, we successfully changed the substrate preference of ClaS from HYQ analogues to PHB analogues, probably comparable with XimB. 31 As the gatekeeper residue His or Arg is conserved in the PHB-type UbiA PTs, it will facilitate us to engineer the PHB-type UbiA PTs by single-residue mutation for the synthesis of preferable prenylated aromatic compounds.…”

“…The UbiA superfamily proteins show similar structural characteristics regardless of different sources and various substrates recognized, and the conserved features are the typical 7–9 predicted transmembrane helices. ,, In addition, they have two characteristic conserved aspartate-rich motifs with the consensus sequences NDxxDxxxD and DxxxD (x stands for any amino acid residues), which are likely involved in Mg 2+ ion binding and prenyl substrate stabilization, ,, and another YxxxK motif may also participate in prenyl substrate binding. , Unlike the soluble ABBA-type and DMATS-type PTs easily being crystallized, , due to the membrane-bound features, only three crystal structures have been reported in the UbiA superfamily, including ApUbiA (PDB: 4OD5) from Aeropyrum pernix, AfUbiA (PDB: 4TQ5) from Archaeoglobus fulgidus, and DGGGP synthase (PDB: 6M31) from Methanocaldococcus jannaschii . Among them, ApUbiA is a typical PHB-type UbiA PT as its complex with Mg 2+ ions, GPP, and PHB was obtained .…”

“…Understanding the structures and catalytic mechanisms of the PHB-type UbiA PTs, particularly the selectivity of prenyl donors and aromatic acceptors, could facilitate their engineering and application. To our knowledge, 16 different soluble aromatic PTs have been crystallized and used for elucidation of protein structures . Their active pockets are surrounded by a unique PT barrel comprising 10 antiparallel β-strands, and the surrounded residues may play important roles in binding the prenyl donors and aromatic substrates, − which provided insights for exploring their substrate selectivity, especially for identification of the gatekeeper residues.…”

“…To our knowledge, 16 different soluble aromatic PTs have been crystallized and used for elucidation of protein structures . Their active pockets are surrounded by a unique PT barrel comprising 10 antiparallel β-strands, and the surrounded residues may play important roles in binding the prenyl donors and aromatic substrates, − which provided insights for exploring their substrate selectivity, especially for identification of the gatekeeper residues. Based on their structures and site-directed mutagenesis, the gatekeeper residues were identified to control the size of the prenyl donor in DMATS-type PTs including AtaPT from Aspergillus terreus, TleC from Streptomyces blastmyceticus, FgaPT2 from Aspergillus fumigatus, and CdpC3PT from Neosartorya fischeri .…”

“…The UbiA superfamily proteins show similar structural characteristics regardless of different sources and various substrates recognized, 12 and the conserved features are the typical 7−9 predicted transmembrane helices. 2,13,14 In addition, they have two characteristic conserved aspartaterich motifs with the consensus sequences NDxxDxxxD and DxxxD (x stands for any amino acid residues), which are likely involved in Mg 2+ ion binding and prenyl substrate stabilization, 2,13,14 and another YxxxK motif may also participate in prenyl substrate binding.…”