C-Diazeniumdiolate Graminine in the Siderophore Gramibactin Is Photoreactive and Originates from Arginine

Biosynthesis and recruitment of reactive amino acids in nonribosomal peptide assembly lines

Reactive amino acid side chains play important roles in the binding of peptides to specific targets. In addition, their reactivity enables selective peptide conjugation and functionalization for pharmaceutical purposes. Diverse reactive amino acids are incorporated into nonribosomal peptides, which serve as a source for drug candidates. Notable examples include (poly)unsaturated (enamine, alkyne, and furyl) and halogenated residues, strained carbacycles (cyclopropyl and cyclopropanol), small heterocycles (oxirane and aziridine), and reactive N-N functionalities (hydrazones, diazo compounds, and diazeniumdiolates). Their biosynthesis requires diverse biocatalysts for sophisticated reaction mechanisms. Several avenues have been identified for their incorporation into peptides, the recruitment by adenylation domains or ligases, on-line modifications, and enzymatic tailoring reactions. Combined with protein engineering approaches, this knowledge provides new opportunities in synthetic biology and bioorthogonal chemistry.

Discovery, isolation, and characterization of diazeniumdiolate siderophores

The C-diazeniumdiolate (N-nitrosohydroxylamine) group in the amino acid graminine (Gra) is a newly discovered Fe(III) ligand in microbial siderophores. Graminine was first identified in the siderophore gramibactin, and since this discovery, other Gra-containing siderophores have been identified, including megapolibactins, plantaribactin, gladiobactin, trinickiabactin (gramibactin B), and tistrellabactins. The C-diazeniumdiolate is photoreactive in UV light which provides a convenient characterization tool for this type of siderophore. This report details the process of genomics-driven identification of bacteria producing Gra-containing siderophores based on selected biosynthetic enzymes, as well as bacterial culturing, isolation and characterization of the C-diazeniumdiolate siderophores containing Gra.

Linking biosynthetic genes to natural products using inverse stable isotopic labeling (InverSIL)

The sequencing of microbial genomes has far outpaced their functional annotation. Stable isotopic labeling can be used to link biosynthetic genes with their natural products; however, the availability of the required isotopically substituted precursors can limit the accessibility of this approach. Here, we describe a method for using inverse stable isotopic labeling (InverSIL) to link biosynthetic genes with their natural products. With InverSIL, a microbe is grown on an isotopically substituted medium to create a fully substituted culture, and subsequently, the incorporation of precursors of natural isotopic abundance can be tracked by mass spectrometry. This eliminates issues with isotopically substituted precursor availability. We demonstrate the utility of this approach by linking a luxI-type acyl-homoserine lactone synthase gene in a bacterium that grows on methanol with its quorum sensing signal products. In the future, InverSIL can also be used to link biosynthetic gene clusters hypothesized to produce siderophores with their natural products.

Elucidation of Chalkophomycin Biosynthesis Reveals N-Hydroxypyrrole-Forming Enzymes

Reactive functional groups, such as N-nitrosamines, impart unique bioactivities to the natural products in which they are found. Recent work has illuminated enzymatic N-nitrosation reactions in microbial natural product biosynthesis, motivating interest in discovering additional metabolites constructed using such reactivity. Here, we use a genome mining approach to identify over 400 cryptic biosynthetic gene clusters (BGCs) encoding homologues of the N-nitrosating biosynthetic enzyme SznF, including the BGC for chalkophomycin, a CuII-binding metabolite that contains a C-type diazeniumdiolate and N-hydroxypyrrole. Characterizing chalkophomycin biosynthetic enzymes reveals previously unknown enzymes responsible for N-hydroxypyrrole biosynthesis, including the first prolyl-N-hydroxylase, and a key step in the assembly of the diazeniumdiolate-containing amino acid graminine. Discovery of this pathway enriches our understanding of the biosynthetic logic employed in constructing unusual heteroatom-heteroatom bond-containing functional groups, enabling future efforts in natural product discovery and biocatalysis.

Chalkophomycin Biosynthesis Revealing Unique Enzyme Architecture for a Hybrid Nonribosomal Peptide Synthetase and Polyketide Synthase

Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable of coordinating cupric ions draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a ~31 kb DNA region, consisting of 19 open reading frames that encode five nonribosomal peptide synthetases (ChmHIJLO), one modular polyketide synthase (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA'CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm-type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.

Elucidation of chalkophomycin biosynthesis reveals N-hydroxypyrrole-forming enzymes

Reactive functional groups, such as N-nitrosamines, impart unique bioactivities to the natural products in which they are found. Recent work has illuminated enzymatic N-nitrosation reactions in microbial natural product biosynthesis, motivating an interest in discovering additional metabolites constructed using such reactivity. Here, we use a genome mining approach to identify over 400 cryptic biosynthetic gene clusters (BGCs) encoding homologs of the N-nitrosating biosynthetic enzyme SznF, including the BGC for chalkophomycin, a CuII-binding metabolite that contains a C-type diazeniumdiolate and N-hydroxypyrrole. Characterizing chalkophomycin biosynthetic enzymes reveals previously unknown enzymes responsible for N-hydroxypyrrole biosynthesis, including the first prolyl-N-hydroxylase, and a key step in assembly of the diazeniumdiolate-containing amino acid graminine. Discovery of this pathway enriches our understanding of the biosynthetic logic employed in constructing unusual heteroatom-heteroatom bond-containing functional groups, enabling future efforts in natural product discovery and biocatalysis.

Photolytic C-Diazeniumdiolate Disassembly in the β-Diketiminate Complexes [MeLM(O2N2CPh3)] (M = Fe, Co, Cu)

The reaction of [K(18-crown-6)][O2N2CPh3] with [MeLCo(μ-Br)2Li(OEt2)] (MeL = {(2,6-iPr2C6H3)NC(Me)}2CH) generates the trityl diazeniumdiolate complex, [MeLCo(O2N2CPh3)] (1), in moderate yield. Similar metathesis reactions result in the formation of the Fe and Cu analogues, [MeLM(O2N2CPh3)] (Fe, 2; Cu, 3), which can also be isolated in moderate yields. Complexes 1-3 were characterized by ultraviolet-visible (UV-vis) spectroscopy, and their solid-state structures were determined by X-ray crystallography. These complexes were further characterized via 1H NMR spectroscopy (in the case of 1 and 2) or EPR spectroscopy (in the case of 3). Irradiation of complexes 1 and 2 with 371 nm light generates the known dinitrosyl complexes, [MeLM(NO)2] (M = Co, 4; Fe, 5), along with Ph3CH and 9-phenylfluorene. We propose that 4 and 5 are formed via the putative hyponitrite intermediates, [MeLM(κ2-O,O-ONNO)], which are formed by photoinduced homolysis of the C-N bond of the [O2N2CPh3] ligand. In contrast, irradiation of complex 3 with 371 nm light, in the presence of 1 equiv of PPh3, led to the formation of the Cu(I) complexes, [MeLCu(PPh3)], [(ArNCMeC(NO)CMeNAr)Cu(PPh3)] (6), and [(ArNCMeC(NO)CMeNAr)Cu]2 (7), of which the latter two are products of γ-nitrosation of the β-diketiminiate ligand. Also formed in this transformation are Ph3CN(H)OCPh3, Ph3PO, and N2O, along with trace amounts of NO.

Tistrellabactins A and B Are Photoreactive C-Diazeniumdiolate Siderophores from the Marine-Derived Strain Tistrella mobilis KA081020-065

The C-diazeniumdiolate group in the amino acid graminine is emerging as a new microbially produced Fe(III) coordinating ligand in siderophores, which is photoreactive. While the few siderophores reported from this class have only been isolated from soil-associated microbes, here we report the first C-diazeniumdiolate siderophores tistrellabactins A and B, isolated from the bioactive marine-derived strain Tistrella mobilis KA081020-065. The structural characterization of the tistrellabactins reveals unique biosynthetic features including an NRPS module iteratively loading glutamine residues and a promiscuous adenylation domain yielding either tistrellabactin A with an asparagine residue or tistrellabactin B with an aspartic acid residue at analogous positions. Beyond the function of scavenging Fe(III) for growth, these siderophores are photoreactive upon irradiation with UV light, releasing the equivalent of nitric oxide (NO) and an H atom from the C-diazeniumdiolate group. Fe(III)-tistrellabactin is also photoreactive, with both the C-diazeniumdiolate and the β-hydroxyaspartate residues undergoing photoreactions, resulting in a photoproduct without the ability to chelate Fe(III).

Reductases Produce Nitric Oxide in an Alternative Pathway to Form the Diazeniumdiolate Group of l-Alanosine

l-Alanosine is a diazeniumdiolate (N-nitrosohydroxylamine) antibiotic that inhibits MTAP-deficient tumor cells by blocking de novo adenine biosynthesis. Previous work revealed the early steps in the biosynthesis of l-alanosine. In the present study, we used genome mining to discover two new l-alanosine-producing strains that lack the aspartate-nitrosuccinate pathway genes found in the original l-alanosine producer. Instead, nitrate is reduced with a unique set of nitrate-nitrite reductases. These enzymes are typically used as part of the nitrogen cycle for denitrification or assimilation, and our report here shows how enzymes from the nitrogen cycle can be repurposed for the biosynthesis of specialized metabolites. The widespread distribution of nitric-oxide-producing reductases also indicates a potential for the discovery of new nitric-oxide-derived natural products.

NO and N2O Release from the Trityl Diazeniumdiolate Complexes [M(O2N2CPh3)3]- (M = Fe, Co)

Reaction of MBr₂ with 3 equiv of [K(18-crown-6)][O₂N₂CPh₃] generates the trityl diazeniumdiolate complexes [K(18-crown-6)][M(O₂N₂CPh₃)₃] (M = Co, 2; Fe, 3) in good yields. Irradiation of 2 and 3 using 371 nm light led to NO formation in 10 and 1% yields (calculated assuming a maximum of 6 equiv of NO produced per complex), respectively. N₂O was also formed during the photolysis of 2, in 63% yield, whereas photolysis of 3 led to the formation of N₂O, as well as Ph₃CN(H)OCPh₃, in 37 and 5% yields, respectively. These products are indicative of diazeniumdiolate fragmentation via both C-N and N-N bond cleavage pathways. In contrast, oxidation of complexes 2 and 3 with 1.2 equiv of [Ag(MeCN)₄][PF₆] led to N₂O formation but no NO formation, suggesting that diazeniumdiolate fragmentation occurs exclusively via C-N bond cleavage under these conditions. While the photolytic yields of NO are modest, they represent a 10- to 100-fold increase compared to the previously reported Zn congener, suggesting that the presence of a redox-active metal center favors NO formation upon trityl diazeniumdiolate fragmentation.

Mining elements of siderophore chirality encoded in microbial genomes

The vast majority of bacteria require iron to grow. A significant iron acquisition strategy is the production of siderophores, which are secondary microbial metabolites synthesized to sequester iron(III). Siderophore structures encompass a variety of forms, of which highly modified peptidic siderophores are of interest herein. State-of-the-art genome mining tools, such as antiSMASH (antibiotics & Secondary Metabolite Analysis SHell), hold the potential to predict and discover new peptidic siderophores, including a combinatoric suite of triscatechol siderophores framed on a triserine-ester backbone of the general class, (DHB-^l/d CAA-^l Ser)₃ (CAA, cationic amino acid). Siderophores with ^l/d Arg, ^l/d Lys and ^l Orn, but not ^d Orn, were predicted in bacterial genomes. Fortuitously the ^d Orn siderophore was identified, yet its lack of prediction highlights the limitation of current genome mining tools. The full combinatoric suite of these siderophores, which form chiral iron(III) complexes, reveals stereospecific coordination chemistry encoded in microbial genomes. The chirality embedded in this suite of Fe(III)-siderophores raises the question of whether the relevant siderophore-mediated iron acquisition pathways are stereospecific and selective for ferric siderophore complexes of a defined configuration.