Yiguang Zhu

Identification and Characterization of Xiamycin A and Oxiamycin Gene Cluster Reveals an Oxidative Cyclization Strategy Tailoring Indolosesquiterpene Biosynthesis

Xiamycin A (XMA) and oxiamycin (OXM) are bacterial indolosesquiterpenes featuring rare pentacyclic ring systems and are isolated from a marine-derived Streptomyces sp. SCSIO 02999. The putative biosynthetic gene cluster for XMA/OXM was identified by a partial genome sequencing approach. Eighteen genes were proposed to be involved in XMA/OXM biosynthesis, including five genes for terpene synthesis via a non-mevalonate pathway, eight genes encoding oxidoreductases, and five genes for regulation and resistance. Targeted disruptions of 13 genes within the xia gene cluster were carried out to probe their encoded functions in XMA/OXM biosynthesis. The disruption of xiaK, encoding an aromatic ring hydroxylase, led to a mutant producing indosespene and a minor amount of XMA. Feeding of indosespene to XMA/OXM nonproducing mutants revealed indosespene as a common precursor for XMA/OXM biosynthesis. Most notably, the flavin dependent oxygenase XiaI was biochemically characterized in vitro to convert indosespene to XMA, revealing an unusual oxidative cyclization strategy tailoring indolosesquiterpene biosynthesis.

Mechanistic Insights into Polycycle Formation by Reductive Cyclization in Ikarugamycin Biosynthesis

Ikarugamycin is a member of the polycyclic tetramate macrolactams (PTMs) family of natural products with diverse biological activities. The biochemical mechanisms for the formation of polycyclic ring systems in PTMs remain elusive. The enzymatic mechanism of constructing an inner five-membered ring in ikarugamycin is reported. A three-gene-cassette ikaABC from the marine-derived Streptomyces sp. ZJ306 is sufficient for conferring ikarugamycin production in a heterologous host. IkaC catalyzes a reductive cyclization reaction to form the inner five-membered ring by a Michael addition-like reaction. This study provides the first biochemical evidence for polycycle formation in PTMs and suggests a reductive cyclization strategy which may be potentially applicable in general to the corresponding ring formation in other PTMs.

New diketopiperazine derivatives from a deep-sea-derived Nocardiopsis alba SCSIO 03039

The strain SCSIO 03039 was isolated from a sediment sample in the Indian Ocean and was characterized as a Nocardiopsis alba species on the basis of its 16S rRNA gene sequence. Seven diketopiperazines (DKPs), including two new DKPs nocazines D (2a) and E (2b), and five known DKPs (1, 3–6), were isolated from N. alba SCSIO 03039, along with two known compounds 2-methoxy-1,4-naphthoquinone (7) and 1-hydroxy-4-methoxy-2-naphthoic acid (8). Their structures were elucidated by mass and NMR spectroscopic analyses. The structure of methoxyneihumicin (1), previously proposed in a conference poster lacking publicly available experimental data, was validated for the first time by detailed NMR analyses and X-ray diffraction study. The two enantiomers nocazines D (2a) and E (2b) were isolated as a mixture. Compounds 3 and 4 were only known as synthetic compounds before. Methoxyneihumicin (1) exhibited in vitro cytotoxicities against MCF-7 and SF-268 with IC50 values of 4.6 and 12.7 μM, respectively, better than those of 6 (22.0 and 20.6 μM). The other compounds showed less pronounced cytotoxities against three tested human cancer cell lines and no compounds displayed antibacterial activities toward four indicator strains.

Dissecting Glycosylation Steps in Lobophorin Biosynthesis Implies an Iterative Glycosyltransferase

The identification of a lobophorin biosynthetic gene cluster from the deep-sea derived Streptomyces sp. SCSIO 01127 reveals a paradigm of three glycosyltransferases (GTs) LobG1-LobG3 being responsible for appending four sugars. Characterization of five differentially glycosylated metabolites from three GT gene-inactivation mutants allowed the assignment of GT functions and the implication of LobG3 as an iterative GT to attach two digitoxoses.

Identification of caerulomycin A gene cluster implicates a tailoring amidohydrolase.

The biosynthetic gene cluster for caerulomycin A (1) was cloned and characterized from the marine actinomycete Actinoalloteichus cyanogriseus WH1-2216-6, which revealed an unusual hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) system. The crmL disruption mutant accumulated caerulomycin L (2) with an extended L-leucine at C-7, implicating an amidohydrolase activity for CrmL. The leucine-removing activity was confirmed for crude CrmL enzymes. Heterologous expression of the 1 gene cluster led to 1 production in Streptomyces coelicolor.

Carboxyl formation from methyl via triple hydroxylations by XiaM in xiamycin A biosynthesis.

The P450 enzyme XiaM was identified as a candidate to form the C-24 carboxyl group in xiamycin A (1). Alteration of medium composition led to the discovery of four new compounds from the ΔxiaM and the ΔxiaK (encoding an aromatic ring hydroxylase) mutants. Biotransformation experiments revealed that XiaM was capable of converting a methyl group to a carboxyl group through diol and aldehyde intermediates.

Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation.

ABSTRACT Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis.

Fluostatins I-K from the South China Sea-Derived Micromonospora rosaria SCSIO N160

The strain SCSIO N160 was isolated from a South China Sea sediment sample and was characterized as a Micromonospora rosaria species on the basis of its 16S rRNA gene sequence. Three new fluostatins, I-K (1-3), were isolated from the culture of M. rosaria SCSIO N160, together with six known compounds, fluostatins C-F (4-7), rabelomycin (8), and phenanthroviridone (9). The structure of fluostatin D (5) was confirmed by an X-ray crystallographic study. The absolute configuration of 1 and 3 was assigned by electronic circular dichroism calculations. Compounds 8 and 9 exhibited good antimicrobial activities against Staphylococcus aureus ATCC 29213 with MIC values of 1.0 and 0.25 μg/mL, respectively. Compound 9 also exhibited significant in vitro cytotoxic activities toward SF-268 (IC50 0.09 μM) and MCF-7 (IC50 0.17 μM).

Heronamides D-F, Polyketide Macrolactams from the Deep-Sea-Derived Streptomyces sp SCSIO 03032

Three new macrolactams, heronamides D-F (1-3), were isolated from the deep-sea-derived Streptomyces sp. SCSIO 03032 upon changing cultivation conditions. The planar structures of heronamides D-F (1-3) were elucidated by extensive MS and NMR spectroscopic analyses and comparisons with the closely related heronamides A-C. The relative configurations of 1-3 were deduced by detailed analysis of (3)JHH values and NOESY data. The absolute configurations of 1 and 2 were determined by chemical modifications and application of the modified Moshers method. None of the compounds exhibited obvious antimicrobial or cytotoxic activities.

Characterization of Heronamide Biosynthesis Reveals a Tailoring Hydroxylase and Indicates Migrated Double Bonds.

Heronamides belong to a growing family of β‐amino acid polyketide macrolactams (βPMs) with an unsaturated side chain. The biosynthetic gene cluster for heronamide F was identified from the deep‐sea‐derived Streptomyces sp. SCSIO 03032. The involvement of the gene cluster in heronamide biosynthesis was confirmed by the functional characterization of the P450 enzyme HerO as an 8‐hydroxylase for tailoring heronamide biosynthesis. The presence of migrated double bonds in the conjugated diene‐containing side chain of heronamides was confirmed by feeding experiments with labeled small carboxylic acid molecules. This study is the first demonstration of migrated double bonds in βPMs with an unsaturated side chain.