In vivo characterization of nonribosomal peptide synthetases NocA and NocB in the biosynthesis of nocardicin A

Abstract

Two nonribosomal peptide synthetases (NRPS), NocA and NocB, together comprising five modules, are essential for the biosynthesis of the D,L,D configured tripeptide backbone of the monocyclic β-lactam nocardicin A. We report a double replacement gene strategy in which point mutations were engineered in the two encoding NRPS genes without disruption of the nocABC operon by placing selective markers in adjacent genes. A series of mutants was constructed to inactivate the thiolation (T) domain of each module and to evaluate an HHxxxDR catalytic motif in NocA and an atypical extended histidine motif in NocB. The loss of nocardicin A production in each of the T domain mutants indicates that all five modules are essential for its biosynthesis. Conversely, production of nocardicin A was not affected by mutation of the NocB histidine motif or the R828G mutation in NocA.

Figure 1

Biosynthesis of nocardicin A in N. uniformis. A. Gene cluster for the biosynthetic pathway which includes genes encoding two NRPSs (blue), tailoring enzymes (red), proteins involved in regulation and transport (violet), proteins involved in biosynthesis of pHPG (green) and proteins shown to be non-essential for nocardicin A biosynthesis (gray) . B. p-HPG biosynthetic pathway. C. Predicted domain and module organization of Noc A and NocB; Substrates predicted by bioinformatic analysis of the A domain active sites are shown. D. Late stage biosynthetic steps; conversion of nocardicin G to nocardicin A.

Figure 2

Biosynthesis of the Arnstein L,L,D-tripeptide, the precursor to isopenicillin N by ACV synthetase. IPNS denotes isopenicillin N synthase.

Figure 3

HPLC chromatograms of the culture supernatents of nocF::apr N. uniformis with and without chemical complementation with L-pHPG compared to wild-type N. uniformis. Key components are tyrosine (retention time = 5 min), p-hydroxybenzoyl formate (retention time = 8.6 min) and nocardicin A (retention time = 14.6 min), indicated by a dot (●).

Figure 4

In vivo 2-Step gene replacement strategy. The first step required the preparation of a deletion mutant. Transformation of the deletion mutant with a vector containing the native or engineered sequence followed by homologous recombination gives the desired mutant. A. Strategy for mutagenesis of nocA in which an apr gene cassette is placed in the adjacent gene nocF. The nocF::apr mutant is chemically complemented by the addition of L-pHPG to the culture medium. B. Strategy for mutagenesis of nocB in which an apr gene cassette is placed in the non-essential gene nocE.

Figure 5

HPLC chromatograms of the culture supernatents from each set of N. uniformis mutants prepared in this study compared to wild-type, analyzed following fermentation for 5 days. In these studies, the culture medium was supplemented with 0.5 mM L-pHPG, except where noted otherwise. The peak for nocardicin A is indicated by a dashed line. A. Chromatograms for deletion mutant T2KO, T domain mutants nocA S626A (T1PM) and nocA S1671A (T2PM), and the native ‘knock-in’ experiment ((+) Cntl), in which the native nocA sequence was restored. B. Chromatograms for deletion mutant T3KO, T domain mutant nocA S2782A (T3PM) and a positive control ((+) Cntl), in which the native nocA sequence was restored compared to wild-type N. unformis. C. Chromatograms for mutant nocA R828G, located in the C2 domain are compared to the deletion mutant T2KO and wild-type N. unformis . For comparison, the chromatogram of the C2PM mutant, grown without pHPG supplementation is shown. D. Chromatograms for deletion mutant T45KO, T domain mutants nocB S571A (T4PM) and nocB S1648A (T5PM), and a positive control ((+) Cntl), in which the native nocB sequence was restored are plotted.

Figure 6

Comparison of extended His motif observed in the NocB A5 domain to the initiation A domains of NRPSs for chloroeremomycin (CepA), balhimycin (BpsA), complestatin (ComA), A47934 (StaA) and teicoplanin (TcpA). Identical residues are shaded. The conserved histidine and acidic residues of the extended His motif are noted with an asterisk (*). Numbers indicate amino acid residues from the N-terminus of the protein. Gene Bank accession numbers are as follows: CepA, AJ223999; BpsA, Y16952; ComA, AF386507; StaA, U82965; TcpA, AJ605139.