An Unusual Protector-Protégé Strategy for the Biosynthesis of Purine Nucleoside Antibiotics

Abstract

Pentostatin (PTN, deoxycoformycin) and arabinofuranosyladenine (Ara-A, vidarabine) are purine nucleoside antibiotics used clinically to treat hematological cancers and human DNA virus infections, respectively. PTN has a 1,3-diazepine ring, and Ara-A is an adenosine analog with an intriguing epimerization at the C-2' hydroxyl group. However, the logic underlying the biosynthesis of these interesting molecules has long remained elusive. Here, we report that the biosynthesis of PTN and Ara-A employs an unusual protector-protégé strategy. To our surprise, we determined that a single gene cluster governs PTN and Ara-A biosynthesis via two independent pathways. Moreover, we verified that PenB functions as a reversible oxidoreductase for the final step of PTN. Remarkably, we provided the first direct biochemical evidence that PTN can protect Ara-A from deamination by selective inhibition of the host adenosine deaminase. These findings expand our knowledge of natural product biosynthesis and open the way for target-directed genome mining of Ara-A/PTN-related antibiotics.

Biosynthesis of 2′-Chloropentostatin and 2′-Amino-2′-Deoxyadenosine Highlights a Single Gene Cluster Responsible for Two Independent Pathways in Actinomadura sp. Strain ATCC 39365

“…More than that, the 2=-Cl PTN/PTN pathway was deduced to be closely related to that of the primary L-histidine (20). The results of this study are consistent with previous work for PTN pathway in S. antibioticus NRRL 3238 (14). Five enzymes, AdaA (SAICAR synthetase), AdaB (short-chain dehydrogenase) AdaC (ATP phosphoribosyltransferase), AdaK (phosphoribosyl isomerase), and AdaL (ATP phosphoribosyltransferase), are assigned as being involved in PTN pathway (Fig.…”

“…ATCC 39365 were subsequently annotated by the Glimmer 3.0 software, yielding 10,533 valid open reading frames (ORFs). As 2=-Cl PTN and PTN share the 1,3-diazepine scaffold, implicating that they harbor the same biosynthetic logic, we thus use the three key enzymes, PenA (ATP phosphoribosyl-transferase), PenB (short-chain dehydrogenase), and PenC (5-amino-4-imidazole N-succinocarboxamide ribonucleotide-5-phosphate [SAICAR] synthetase) (14), in the PTN biosynthetic pathway as probes to conduct individual BLASTP analysis against the genome of Actinomadura sp. ATCC 39365, which leads to the location of the only one candidate gene cluster encoding enzymes involving ORF02747 (designated AdaC, 58% identity to PenA), ORF02756 (AdaL, 53% identity to PenA), ORF02748 (AdaB, 70% identity to PenB), and ORF02749 (AdaA, 72% identity to PenC) ( Table 1).…”

“…To address which adenosine deaminase of the host contributes to the phenotypes, we thus selected a versatile Ara-A/adenosine deaminase from S. antibioticus, SanADA3 (accession no. KT591401) (14), as a probe to conduct BLASTP analysis against the genome of Actinomadura sp. ATCC 39365, which leads to the identification of four homologs.…”

“…After dephosphorylation by AdaM or an unknown enzyme, compound 6 is dehydrogenated by AdaB (PenB homolog) to produce the target product, PTN (Fig. 6A) (14).…”

“…In addition, the C-7 origin of the "fat" 1,3-diazepine ring comes from C-1 of D-ribose by inserting the N-1 and C-6 of the intact purine ring (7). In our recent report, we revealed that a single gene cluster is involved in two independent pathways during PTN and Ara-A biosynthesis, and we further demonstrated that their biosynthesis employs a protector-protégé strategy, with PTN capable of protecting Ara-A from deamination by the host adenosine deaminase (14). Notably, 2=-Cl PTN has been reported as the first naturally occurring nucleoside natural product bearing the chloro group (15).…”