A Single Gene Cluster for Chalcomycins and Aldgamycins: Genetic Basis for Bifurcation of Their Biosynthesis

Abstract

Aldgamycins are 16-membered macrolide antibiotics with a rare branched-chain sugar d-aldgarose or decarboxylated d-aldgarose at C-5. In our efforts to clone the gene cluster for aldgamycins from a marine-derived Streptomyces sp. HK-2006-1 capable of producing both aldgamycins and chalcomycins, we found that both are biosynthesized from a single gene cluster. Whole-genome sequencing combined with gene disruption established the entire gene cluster of aldgamycins: nine new genes are incorporated with the previously identified chalcomycin gene cluster. Functional analysis of these genes revealed that almDI/almDII, (encoding α/β subunits of pyruvate dehydrogenase) triggers the biosynthesis of aldgamycins, whereas almCI (encoding an oxidoreductase) initiates chalcomycins biosynthesis. This is the first report that aldgamycins and chalcomycins are derived from a single gene cluster and of the genetic basis for bifurcation in their biosynthesis.

Characterization of Methyltransferase AlmCII in Chalcomycin Biosynthesis: The First TylF Family O‐Methyltransferase Works on a 4′‐Deoxysugar

“…The molecular formulas of compounds 7 and 8 were established as C 34 H 56 O 14 and C 34 H 54 O 14 by the quasi‐molecular ions at m / z 711.3572 [ M +Na] + and 709.3397 [ M +Na] + in HR‐ESI‐MS, which were 14 amu (CH 2 ) fewer than for 3 and 4 , respectively. The 1 H and 13 C NMR spectra of 7 were very similar to those of 3 except that the signal of a methoxy group [ δ C =56.7 ppm/ δ H =3.42 ppm (3 H, S)] linked to C‐3′ in 3 was not observed in 7 , and there was a significant upfield shift of C‐3′ in 7 compared to 3 (from δ C =80.5 ppm to δ C =71.2 ppm), thus implying that the C‐3′ methoxy group in 3 had become a hydroxy group in 7 . Moreover, the structure of 7 was further confirmed by 2D NMR analyses (Table S3 ), with the assignments of all proton and carbon resonances provided in Table .…”

“…The resulting plasmid was then transformed into Streptomyces sp. HK‐2006‐1 by intergeneric conjugation as described previously . Successful knock‐out of the almCII gene in a clone named JHZ1007 was confirmed by genotyping PCR with primers almCII ‐EcoRI‐F and almCII ‐BamHI‐R.…”

“…In our previous effort to clone the gene cluster for aldgamycins, which have an identical skeletal structure to that of chalcomycins but with a distinct sugar substituent at C‐5 ( d ‐aldgarose in aldgamycins and d ‐chalcose in chalcomycins), we found that they are biosynthesized from a single gene cluster . Bioinformatics analysis of the gene cluster revealed that there are four methyltransferases (AlmEIV, AlmEIII, AlmCII, and AlmUI).…”

“…[2] The TylF family( PF05711) represents al arge group of class I SAM-dependent methyltransferases, which currently contains 620 sequences spanning 468 species in the Pfam database. [3] Thus far,o nly about1 9e nzymes, including TylF, [4] MycF, [5] ChmMII, [6] GerMII, [7] AlmEIII, [8] NovP, [9] CouP, [10] CloP, [1a] SpnH, [11] BusH, [12] SnogL, [13] ElmMII, [14] Cpz29, [15] LobS1, [1c] Mra5, [16] LipZ, [17] Rmt4, MtfB, and MtfC, [18] have been functionally assigned by either experiment or homology-based analysis( Figure S1 in the SupportingI nformation). To our surprise, all of these characterized enzymes exhibited high regioselectivity,o nly methylating hydroxy groupsa tp osition3 or 4o ft he sugar pyranose ring.…”

Chalcomycins from Marine-Derived Streptomyces sp. and Their Antimicrobial Activities

“…Among our recent discoveries [11,12,13,14,15,16,17,18,19,20,21], we recently reported that a strain of Streptomyces sp. HK-2006-1 produced both aldgamycins and chalcomycins, which are 16-membered macrolides [11,21]. Chalcomycin and seven aldgamycins were isolated from this strain, and chalcomycin showed more potent antibacteria activity against Staphylococcus aureus than aldgamycins [11].…”