Echinocandin B biosynthesis: a biosynthetic cluster from Aspergillus nidulans NRRL 8112 and reassembly of the subclusters Ecd and Hty from Aspergillus pachycristatus NRRL 11440 reveals a single coherent gene cluster

Abstract

BackgroundEchinocandins are nonribosomal lipopeptides produced by ascommycete fungi. Due to their strong inhibitory effect on fungal cell wall biosynthesis and lack of human toxicity, they have been developed to an important class of antifungal drugs. Since 2012, the biosynthetic gene clusters of most of the main echinocandin variants have been characterized. Especially the comparison of the clusters allows a deeper insight for the biosynthesis of these complex structures.ResultsIn the genome of the echinocandin B producer Aspergillus nidulans NRRL 8112 we have identified a gene cluster (Ani) that encodes echinocandin biosynthesis. Sequence analyses showed that Ani is clearly delimited from the genomic context and forms a monophyletic lineage with the other echinocandin gene clusters. Importantly, we found that the disjunct genomic location of the echinocandin B gene cluster in A. pachycristatus NRRL 11440 on two separate subclusters, Ecd and Hty, at two loci was likely an artifact of genome misassembly in the absence of a reference sequence. We show that both sequences can be aligned resulting a single cluster with a gene arrangement collinear compared to other clusters of Aspergillus section Nidulantes. The reassembled gene cluster (Ecd/Hty) is identical to a putative gene cluster (AE) that was previously deposited at the NCBI as a sequence from A. delacroxii NRRL 3860. PCR amplification of a part of the gene cluster resulted a sequence that was very similar (97 % identity), but not identical to that of AE.ConclusionsThe Echinocandin B biosynthetic cluster from A. nidulans NRRL 8112 (Ani) is particularly similar to that of A. pachycristatus NRRL 11440 (Ecd/Hty). Ecd/Hty was originally reported as two disjunct sub-clusters Ecd and Hty, but is in fact a continuous sequence with the same gene order as in Ani. According to sequences of PCR products amplified from genomic DNA, the echinocandin B producer A. delacroxii NRRL 3860 is closely related to A. pachycristatus NRRL 11440. A PCR-product from the gene cluster was very similar, but clearly distinct from the sequence published for A. delacroxii NRRL 3860 at the NCBI (No. AB720074). As the NCBI entry is virtually identical with the re-assembled Ecd/Hty cluster, it is likely that it originates from A. pachycristatus NRRL 11440 rather than A. delacroxii NRRL 3860.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2885-x) contains supplementary material, which is available to authorized users.

Structural diversity in echinocandin biosynthesis: the impact of oxidation steps and approaches toward an evolutionary explanation

“…According to this study, the genes are arranged in two separate partial clusters (Ecd and Hty) located on different contigs of the assembly. However, we showed recently that Ecd and Hty can be aligned to a single cluster (Ecd/ Hty) and the disjunct genomic location of the cluster fragments was likely an artifact of genome misassembly in the absence of a reference genome [14]. It was also found that Ecd/Hty was virtually identical with a putative echinocandin B biosynthetic cluster AE deposited at the NCBI as a sequence of the producer strain Aspergillus delacroxii NRRL 3860 (formerly Emericella nidulans var.…”

“…Table 5). Sequence analysis of PCR samples from the genomes of both strains, showed that the sequence of AE cluster is identical with that of A. pachycristatus, but not with A. delacroxii [14]. Moreover, a comparison of the calmodulin genes, a common taxonomic marker for fungi, suggested that strain NRRL 3860 belongs to the Aspergillus 40% feces, < 15% urine (< 1% unchanged) Tolerance Due to their specific mode of action, echinocandins are comparatively well tolerated.…”

“…One compound, pneumocandin A 4 , had already been characterized before and is the most reduced pneumocandin main product produced by a G. lozoyensis strain (ATCC 20988). Even more degenerate is 'compound 14' (suggested name: pneumocandin B 14 ) isolated from G. lozoyensis ΔhT3H. Compared to pneumocandin A 0 , its biosynthesis requires nine of 14 synthetic enzymes, including just two of the six oxygenases (PH, GH).…”

“…However, a more detailed investigation will be necessary to clarify the species affiliation [14,15].…”

Cryptic Production of trans -3-Hydroxyproline in Echinocandin B Biosynthesis

“…The biosynthetic gene cluster of this strain has been identified and comprehensively characterized by the groups of Tang and Walsh (16,17). More recently, the sequence has been revised (21).…”