Identification of functionally clustered nystatin-like biosynthetic genes in a rare actinomycetes, Pseudonocardia autotrophica

Abstract

The polyene antibiotics, including nystatin, pimaricin, amphotericin, and candicidin, comprise a family of very valuable antifungal polyketide compounds, and they are typically produced by soil actinomycetes. Previously, using a polyene cytochrome P450 hydroxylasespeciWc genome screening strategy, Pseudonocardia autotrophica KCTC9441 was determined to contain genes potentially encoding polyene biosynthesis. Here, sequence information of an approximately 125.7-kb contiguous DNA region in Wve overlapping cosmids isolated from the P. autotrophica KCTC9441 genomic library revealed a total of 23 open reading frames, which are presumably involved in the biosynthesis of a nystatin-like compound tentatively named NPP. The deduced roles for six multimodular polyketide synthase (PKS) catalytic domains were found to be highly homologous to those of previously identiWed nystatin biosynthetic genes. Low NPP productivity suggests that the functionally clustered NPP biosynthetic pathway genes are tightly regulated in P. autotrophica. Disruption of a NPP PKS gene completely abolished both NPP biosynthesis and antifungal activity against Candida albicans, suggesting that polyene-speciWc genome screening may constitute an eYcient method for isolation of potentially valuable previously identiWed polyene genes and compounds from various rare actinomycetes widespread in nature.

Selvamicin, an atypical antifungal polyene from two alternative genomic contexts

“…The bioinformatically identified selvamicin cluster resembles known type I PKS-derived polyene BGCs (30)(31)(32)(33)(34)(35), and a side-by-side comparison with the well-characterized nystatin BGC (36,37) readily reveals the origins of selvamicin's unusual structural features (Fig. 5).…”

Production of the antibiotic FR-008/candicidin in Streptomyces sp. FR-008 is co-regulated by two regulators, FscRI and FscRIV, from different transcription factor families

“…PikD, the only regulator in the pikromycin cluster, positively regulates the production of pikromycin in Streptomyces venezuelae (Wilson et al, 2001). In some cases, multiple LAL-type regulators are present in the same cluster, especially in polyene antibiotic biosynthetic clusters, such as NysRI-NysRIII of the nystatin cluster in S. noursei ATCC 11455 (Sekurova et al, 2004), AmphRI-AmphRIII of the amphotericin pathway in S. nodosus (Carmody et al, 2004), NppRI-NppRIII of the NPP cluster in Pseudonocardia autotrophica (Kim et al, 2009) and CanORF1-CanORF3 of the candicidin pathway in Streptomyces griseus (Campelo & Gil, 2002). Most of the time, these LAL-type regulators are clustered with a PimM-like regulator, as seen in the biosynthetic gene clusters for nystatin, amphotericin and NPP (Carmody et al, 2004;Kim et al, 2009;Sekurova et al, 2004).…”

Polyene macrolide biosynthesis in streptomycetes and related bacteria: recent advances from genome sequencing and experimental studies

“…Candicidin is frequently re-isolated and its biosynthetic gene cluster appears in several genomes (Jorgensen et al, 2009;Seipke et al, 2011b;Olano et al, 2014;Tang et al, 2015;Komaki et al, 2015;Liu et al, 2015a). Since the sequencing of the nystatin biosynthetic genes in S. noursei (Brautaset et al, 2000), at least three other closely related clusters have been found (Kim et al, 2009;Barke et al, 2012;Cui et al, 2015). Pimaricin is produced by S. natalensis, Streptomyces gilvosporus, Streptomyces lydicus and Streptomyces chattanoogensis (Aparicio et al, 2016).…”