Coordinated Biosynthesis of the Purine Nucleoside Antibiotics Aristeromycin and Coformycin in Actinomycetes

Abstract

Purine nucleoside antibiotic pairs, concomitantly produced by a single strain, are an important group of microbial natural products. Here, we report a target-directed genome mining approach to elucidate the biosynthesis of the purine nucleoside antibiotic pair aristeromycin (ARM) and coformycin (COF) in DSM 45626 (a new producer for ARM and COF) and NBRC 13005 (a new COF producer). We also provide biochemical data that MacI and MacT function as unusual phosphorylases, catalyzing an irreversible reaction for the tailoring assembly of neplanocin A (NEP-A) and ARM. Moreover, we demonstrate that MacQ is shown to be an adenosine-specific deaminase, likely relieving the potential "excess adenosine" for producing cells. Finally, we report that MacR, an annotated IMP dehydrogenase, is actually an NADPH-dependent GMP reductase, which potentially plays a salvage role for the efficient supply of the precursor pool. Hence, these findings illustrate a fine-tuned pathway for the biosynthesis of ARM and also open the way for the rational search for purine antibiotic pairs. ARM and COF are well known for their prominent biological activities and unusual chemical structures; however, the logic of their biosynthesis has long been poorly understood. Actually, the new insights into the ARM and COF pathway will not only enrich the biochemical repertoire for interesting enzymatic reactions but may also lay a solid foundation for the combinatorial biosynthesis of this group of antibiotics via a target-directed genome mining strategy.

Comparative Investigation into Formycin A and Pyrazofurin A Biosynthesis Reveals Branch Pathways for the Construction of C -Nucleoside Scaffolds

“…Identification of FOR-A gene clusters from diverse actinobacteria. COF and PTN, which have a significant structural resemblance, were recently revealed to share highly similar biosynthetic pathways (18). To identify the target gene clusters for FOR-A biosynthesis, we sequenced the genomes of Nocardia interforma ATCC 21072 and S. kaniharaensis ATCC 21070 using the Illumina method, which rendered ca.…”

“…raw data were processed to render the resulting clean reads, which were assembled by using Velvet software (v1.2.07) to obtain the scaffold. Detailed methods and programs used for genome annotations and accurate bioinformatic analysis were performed according to protocols described previously by Xu et al (18).…”

Comparative investigation into formycin A and pyrazofurin A biosynthesis reveals branch pathways for the construction ofC-nucleoside scaffolds

“…FOR-A and COF were formerly reported to be co-produced by the actinobacteria, Nocardia interforma ATCC 21072 and S. kaniharaensis ATCC 21070 (7, 10), implicating that the genes for their biosyntheses, as those of other purine nucleoside antibiotic pairs, should also constitute a gene cluster (11, 12), Additionally, COF and PTN, featuring significant structural resemblance, were recently revealed to share highly-similar biosynthetic pathways (20).…”

The Biosynthetic Gene Cluster of Pyrazomycin—A C‐Nucleoside Antibiotic with a Rare Pyrazole Moiety

“…To elucidate the origin of the N−N bond in the pyrazole structure, we began by sequencing the genome of the PZN‐producing strain Streptomyces candidus NRRL 3601, and identified a ≈28 kb gene cluster as a candidate for the PZN biosynthetic gene cluster, which we name here as the pyr cluster (Figure A, Table S1 in the Supporting Information). This gene cluster contains a four‐gene subcluster ( pyrOPQS ) that has been linked to the biosynthesis of coformycin, the production of which seems to be associated with many nucleoside family natural products (Figure S1 A) . Moreover, the pyr cluster also contains pyrE , which shows sequence homology to genes that encode (β‐ribofuranosylamino)benzene 5′‐phosphate (β‐RFAP) synthase.…”