Engineered biosynthesis of an ansamycin polyketide precursor in Escherichia coli

Abstract

Ansamycins such as rifamycin, ansamitocin, and geldanamycin are an important class of polyketide natural products. Their biosynthetic pathways are especially complex because they involve the formation of 3-amino-5-hydroxybenzoic acid (AHBA) followed by backbone assembly by a hybrid nonribosomal peptide synthetase/polyketide synthase. We have reconstituted the ability to synthesize 2,6-dimethyl-3,5,7-trihydroxy-7-(3'-amino-5'-hydroxyphenyl)-2,4-heptadienoic acid (P8/1-OG), an intermediate in rifamycin biosynthesis, in an extensively manipulated strain of Escherichia coli. The parent strain, BAP1, contains the sfp phosphopantetheinyl transferase gene from Bacillus subtilis, which posttranslationally modifies polyketide synthase and nonribosomal peptide synthetase modules. AHBA biosynthesis in this host required introduction of seven genes from Amycolatopsis mediterranei, which produces rifamycin, and Actinosynnema pretiosum, which produces ansamitocin. Because the four-module RifA protein (530 kDa) from the rifamycin synthetase could not be efficiently produced in an intact form in E. coli, it was genetically split into two bimodular proteins separated by matched linker pairs to facilitate efficient inter-polypeptide transfer of a biosynthetic intermediate. A derivative of BAP1 was engineered that harbors the AHBA biosynthetic operon, the bicistronic RifA construct and the pccB and accA1 genes from Streptomyces coelicolor, which enable methylmalonyl-CoA biosynthesis. Fermentation of this strain of E. coli yielded P8/1-OG, an N-acetyl P8/1-OG analog, and AHBA. In addition to providing a fundamentally new route to shikimate and ansamycin-type compounds, this result enables further genetic manipulation of AHBA-derived polyketide natural products with unprecedented power.

Fig. 1.

Structures of natural (rifamycin B, ansamitocin P-3, and geldanamycin) and semisynthetic (rifampicin) ansamycin antibiotics.

Fig. 2.

Proposed pathway for AHBA biosynthesis. AminoDHS, 5-amino analog of 3-dehydroshikimic acid; aminoDAHP, 3,4-dideoxy-4-amino-d-arabino-heptulosonic acid 7-phosphate; PEP, phosphoenolpyruvic acid; aminoDHQ, 5-deoxy-5-amino-3-dehydroquinic acid.

Fig. 3.

Proposed pathway for P8/1-OG and rifamycin B biosynthesis. A, adenylation domain; T, thiolation domain; KS, ketosynthase; AT, acyltransferase; DH, dehydratase; KR, ketoreductase.

Fig. 4.

Purified AHBA biosynthesis and engineered RifA proteins. (A) Lane 1, protein marker; lane 2, RifH (49 kDa); lane 3, RifK (43 kDa); lane 4, RifL (40 kDa); lane 5, RifM (26 kDa); lane 6, RifN (33 kDa). (B) Lane 1, protein marker; lane 2, asm47 (38 kDa); lane 3, asm23 (19 kDa). (C) Lane 1, protein marker; lane 2, RifLM+RifM1+M2C (246 kDa); lane 3, M3N+RifM2+RifM3 (301 kDa).

Fig. 5.

(A) Plasmid map of pKW256 for the expression of AHBA biosynthetic proteins. (B) Protein engineering of RifA. (C) Plasmid map of pKW244 for the expression of RifA as two separate proteins. A, adenylation domain; T, thiolation domain; KS, ketosynthase; AT, acyltransferase; DH, dehydratase; KR, ketoreductase.