Biosynthesis and incorporation of an alkylproline-derivative (APD) precursor into complex natural products

Abstract

Covering: up to 2017This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin. These structurally and functionally diverse groups of complex natural products all incorporate rarely occurring 4-alkyl-l-proline derivatives (APDs) biosynthesized from l-tyrosine through an unusual specialized pathway catalysed by a common set of six proteins named Apd1-Apd6. We give an overview of APD formation, which involves unusual enzyme activities, and its incorporation, which is based either on nonribosomal peptide synthetase (PBDs, hormaomycin) or a unique hybrid ergothioneine-dependent condensation system followed by mycothiol-dependent sulphur atom incorporation (lincosamides). Furthermore, within the public databases, we identified 36 novel unannotated biosynthetic gene clusters that putatively encode the biosynthesis of APD compounds. Their products presumably include novel PBDs, but also novel classes of APD compounds, indicating an unprecedented potential for the diversity enhancement of these functionally versatile complex metabolites. In addition, phylogenetic analysis of known and novel gene clusters for the biosynthesis of APD compounds allowed us to infer novel evolutionary hypotheses: Apd3 methyltransferase originates from a duplication event in a hormaomycin biosynthetic gene cluster ancestor, while putative Apd5 isomerase is evolutionarily linked to PhzF protein from the biosynthesis of phenazines. Lastly, we summarize the achievements in preparing hybrid APD compounds by directing their biosynthesis, and we propose that the number of nature-like APD compounds could by multiplied by replacing l-proline residues in various groups of complex metabolites with APD, i.e. by imitating the natural process that occurs with lincosamides and PBDs, in which the replacement of l-proline for APD has proved to be an evolutionary successful concept.

Comparative effects of trifluoromethyl- and methyl-group substitutions in proline

“…88 A notable fact is that 4-methylprolines are abundant in natural products, 89,90 and these are the simplest alkylproline derivatives among others occurring in nature. 91 Another common modification is hydroxylation in position 4; finally extensive experimental data have addressed 4-fluoroprolines. 19,20 For this reason, we compared the lipophilicity of the 4-substituted proline derivatives in Fig.…”

Novel pathway of 3-hydroxyanthranilic acid formation in limazepine biosynthesis reveals evolutionary relation between phenazines and pyrrolobenzodiazepines

“…PhzF and APD biosynthetic protein Lim13 and its homologues from other APD pathways (thereinafter referred to as Apd5 according to the order of the catalysed reaction in APD biosynthesis; see Fig. 3c and a review) 36 belong to the protein family of isomerases together with primary metabolic proline racemases 37 and diaminopimelate (DAP) epimerases 38 . The mutual sequence homology of Apd5 and PhzF (up to 30% of identity); however, significantly exceeds homologies of these proteins to the above mentioned primary metabolic isomerases (13 to 16% of identity).…”

“…That is because Apd5 is encoded within limazepines and all four additional characterized (Fig. 5 ) as well as all 19 hypothetical 36 BGCs of PBDs with an APD moiety. This obligatory presence of Apd5 has a functional explanation: isomerization reaction putatively catalysed by Apd5 results in a planar conformation of the side chain of APD precursors and consequently in the planar shape of the final PBD molecules, which thus fits perfectly within the target structure, i.e.…”

Beyond self-resistance: ABCF ATPase LmrC is a signal-transducing component of an antibiotic-driven signaling cascade hastening the onset of lincomycin biosynthesis

“…BGCs encoding structurally highly related natural lincosamide antibiotics celesticetin and lincomycin represent such a pair, mentioned above, with minimal vs. a complex set of resistance genes (12,26). Based on our knowledge of biosynthesis of both lincosamide antibiotics and a comparative analysis of the respective BGCs (Figure 1a, for review, see (27)), there is only one non-biosynthetic gene, ccr1, in celesticetin BGC, coding for Ccr1 23S rRNA mono-methyltransferase, which is a self-protecting resistance protein modifying the ribosomal target of the producing strain. In contrast, there are four putative nonbiosynthetic genes in lincomycin BGC: the resistance gene, lmrB, homologous to ccr1, a gene encoding the LmbU transcriptional regulator (28,29), and two putative resistance genes coding for a transporter of the major facilitator family, LmrA, and an ABCF protein, LmrC.…”