Cameo appearances of aminoacyl-tRNA in natural product biosynthesis

Abstract

The breadth of unprecedented enzymatic reactions performed during the formation of microbial natural products has continued to expand as new biosynthetic gene clusters are unearthed by genome mining. Enzymes that use aminoacyl-tRNA (aa-tRNA) outside of the translation machinery have been known for decades, and accounts of their use in natural product biosynthesis are just beginning to accumulate. This review will highlight the recent discoveries and advances in our mechanistic understanding of aa-tRNA-dependent enzymes that play key roles in the biosynthesis of a growing number of microbial natural products.

Figure 1

(a) General cyclodipeptide synthase reaction scheme using AlbC from Streptomyces noursei as an example. The reaction proceeds via a dipeptidyl-enzyme intermediate covalently linked to the indicated conserved serine. (b) Proposed mechanism and active site residues involved in the AlbC interaction with two Phe-tRNA^Phe substrates. Figure adapted from [24].

Figure 2

Proposed mechanism of aminoacyl transfer in the activity of FemX_Wv and MprF, along with the diverse reactions performed by homologous biosynthetic enzymes involved in natural product biosynthesis. Streptothricin F (which is produced by NRPS machinery) is shown for comparison with the derivative BD-12. The atoms of the final natural product that originated from aminoacyl-tRNA-dependent activity are highlighted in red.

Figure 3

Proposed mechanism of glutamylation and elimination by LanB dehydratases during biosynthesis of the lantibiotics nisin and microbisporicin. Ser and Thr residues in a precursor peptide are glutamylated in a Glu-tRNA^Glu-dependent reaction. The glutamate is then eliminated to generate dehydroalanine and dehydrobutyrine redidues. The inset next to microbisporicin A1 shows the sequence of the tRNA acceptor stems for Microbispora and E. coli tRNA^Glu with bases predicted to be important for recognition highlighted in red. The glutamate elimination reaction is shown as a concerted process but could involve an enolate intermediate. After dehydration, other enzymes carry out additional post-translational modifications (PTMs) that result in the structures shown at the bottom. The structures for the shorthand notations used in the nisin and microbisporicin drawings are shown.

Figure 4

Proposed activity of split-LanB dehydratases. The split-LanBs act on their substrates as part of a hybrid system with thiazole/oxazole-forming machinery. The proposed mechanism for the heterocycle formation from two dehydroalanine residues is shown.