Identification of a gene cluster that directs putrebactin biosynthesis in Shewanella species: PubC catalyzes cyclodimerization of N-hydroxy-N-succinylputrescine

Putrebactin is a dihydroxamate iron chelator produced by the metabolically versatile marine bacterium Shewanella putrefaciens. It is a macrocyclic dimer of N-hydroxy-N-succinyl-putrescine (HSP) and is structurally related to desferrioxamine E, which is a macrocyclic trimer of N-hydroxy-N-succinyl-cadaverine (HSC). We recently showed that DesD, a member of the NIS synthetase superfamily, catalyzes the key step in desferrioxamine E biosynthesis: ATP-dependent trimerisation and macrocylization of HSC. Here we report identification of a conserved gene cluster in the sequenced genomes of several Shewanella species, including Shewanella putrefaciens, which is hypothesized to direct putrebactin biosynthesis from putrescine, succinyl-CoA and molecular oxygen. The pubC gene within this gene cluster encodes a protein with 65% similarity to DesD. We overexpressed pubC from Shewanella species MR-4 and MR-7 in E. coli. The resulting His6-PubC fusion proteins were purified by Ni-NTA affinity and gel filtration chromatography. The recombinant proteins were shown to catalyze ATP-dependent cyclodimerization of HSP to form putrebactin. The uncyclized dimer of HSP pre-putrebactin was shown to be an intermediate in the conversion of two molecules of HSP to putrebactin. The data indicate that pre-putrebactin is converted to putrebactin via PubC-catalyzed activation of the carboxyl group by adenylation, followed by PubC-catalyzed nucleophilic attack of the amino group on the carbonyl carbon of the acyl adenylate. This mechanism for macrocycle formation is very different from the mechanism involved in the biosynthesis of many other macrocyclic natural products, where already-activated acyl thioesters are converted by thioesterase domains of polyketide synthases and nonribosomal peptide synthetases to macrocycles via covalent enzyme bound intermediates. The results of this study demonstrate that two closely related enzymes, PubC and DesD, catalyze specific cyclodimerization and cyclotrimerization reactions, respectively, of structurally similar substrates, raising intriguing questions regarding the molecular mechanism of specificity.     

Formylation domain: an essential modifying enzyme for the nonribosomal biosynthesis of linear gramicidin

Formylation is an important part of ribosomal peptide synthesis of prokaryotes. In nonribosomal peptide synthesis, however, N-formylation is rather unusual and therefore so far unexplored. In this work, the first module of the linear gramicidin nonribosomal peptide synthetase, LgrA1, consisting of a hypothetical formylation domain, an adenylation, and a peptidyl carrier protein domain was tested for formyltransferase activity in vitro. We demonstrate here that the putative formylation domain does indeed transfer the formyl group of formyltetrahydrofolate (fH4F) onto the first amino acid valine using both cofactors N10- and N5-fH4F, respectively. Most important, the necessity of the formylated starter unit formyl-valine for the initiation of the gramicidin biosynthesis was tested by elongation assays with the bimodular system from LgrA. By omitting the formyl group donor, no condensation product of valine with the subsequent building block glycine was detected, whereas the dipeptide formyl-valyl-glycine was found when assayed in the presence of either formyl donor. The proven formylation activity of the first domain of LgrA represents a novel tailoring enzyme in nonribosomal peptide synthesis.     

Taxol biosynthesis: tyrocidine synthetase A catalyzes the production of phenylisoserinyl CoA and other amino phenylpropanoyl thioesters

In Taxus plants the biosynthesis of the pharmaceutical paclitaxel includes the transfer of β-amino phenylpropanoyls from coenzyme A to the diterpenoid baccatin III by an acyl CoA-dependent acyltransferase. Several enzymes on the pathway are known, yet a few remain unidentified, including the putative ligase that biosynthesizes key β-amino phenylpropanoyl CoAs. The multienzyme, nonribosomal peptide synthetase that produces tyrocidines contains a tridomain starter module tyrocidine synthetase A that normally activates (S)-α-Phe to an adenylate anhydride in the adenylation domain. The Phe moiety is then thioesterified by the pendent pantetheine of the adjacent thiolation domain. Herein, the adenylation domain was found to function as a CoA ligase, making α-, β-phenylalanyl, and phenylisoserinyl CoA. The latter two are substrates of a phenylpropanoyltransferase on the biosynthetic pathway of the antimitotic paclitaxel.     

Stereochemical diversity through cyclodimerization: synthesis of polyketide-like macrodiolides

[reaction: see text] An expeditious procedure for the direct formation of stereochemically well-defined macrodiolides is described. Cyclodimerizations of enantioenriched C7 and C8 hydroxy esters 6 in the presence of catalytic amounts of distannoxane transesterification catalysts afford 14- to 22-membered macrodiolides 7-9 bearing up to six stereocenters. Additional structural diversity is introduced by further stereoselective reactions on selected macrodiolides 7a, 7g, 10a, and 11.     

Synthesis of readily modifiable cyclodextrin analogues via cyclodimerization of an alkynyl-azido trisaccharide

A convergent strategy for the synthesis of beta-cyclodextrin analogues is reported, utilizing preferential cyclodimerization of an azido-alkyne trisaccharide via Cu(I)-catalyzed [3 + 2] dipolar cycloaddition of the alkyne and azide functional groups. The resultant oligosaccharide macrocycle retains the binding propensity of cyclodextrins, as demonstrated by the similar ANS association constants measured for macrocycle 1 and beta-cyclodextrin. This new synthetic strategy opens up new avenues for modular preparation of functionally diverse cyclodextrin analogues that are otherwise inaccessible.     

On the mechanism of the nickel-catalysed regioselective cyclodimerization of isoprene

A study of various Ni-ligand catalysed oligomerizations of isoprene has shown that with π-acidic P ligands the selectivity to cyclodimers amount to 97%. A new type of ligand is introduced, viz. fluoroalkyl phosphites having π-acceptor properties comparable to those of, e.g. PCl₃. With tris(hexafluoroisopropyl) phosphite the main product is 1,4-dimethy1-4-vinylcyclohexene. A detailed explanation based on a two-step mechanism is given. As to the first step, for a series of ligands having similar steric properties the changes in product distribution as a function of the electronic ligand parameter are explained in terms of a gradual change in HOMO-LUMO interactions between Ni and the olefins, with strong π-acidic ligands promoting the head-to-head coupling of the isoprene molecules. The second step, involving reductive elimination of a cyclodimer from the metal, shows an increasing selectivity towards substituted cyclohexenes for the head-to-head and tail-to-tail intermediates with increasing π-acidity of the ligand. The qualitative orbital treatment presented as an explanation is also applicable to reactions found for other metallacyclopentanes.     

Rhodium-catalyzed asymmetric cyclodimerization of oxabenzonorbornadienes and azabenzonorbornadienes: scope and limitations

Cationic rhodium(I)-catalyzed cyclodimerization of oxabenzonorbornadienes produced naphtho[1,2-b]furan ring systems in a single step with excellent yields and excellent enantioselectivities. The effect of various Rh(I) catalysts, Ag(I) salts, solvents, and phosphine ligands on the yield and enantioselectivity of the reaction was investigated, and the scope and limitations of this reaction with various oxabicyclic alkenes were studied. Similar results were obtained with the azabenzonorbornadiene analogues, providing the corresponding cyclodimerization products in excellent yields and excellent enantioselectivities.     

Petrobactin biosynthesis: AsbB catalyzes condensation of spermidine with N8-citryl-spermidine and its N1-(3,4-dihydroxybenzoyl) derivative

The AsbB enzyme, which is involved in the biosynthesis of the virulence-conferring siderophore petrobactin in Bacillus anthracis, is shown to catalyze efficient ATP-dependent condensation of spermidine, but not N(1)-(3,4-dihydroxbenzoyl)-spermidine, with N(8)-citryl-spermidine or N(1)-(3,4-dihydroxbenzoyl)-N(8)-citryl-spermidine, suggesting that N(1)-(3,4-dihydroxbenzoyl)-spermidine is very unlikely to be a significant intermediate in petrobactin biosynthesis, contrary to previous suggestions.     

Assembly line enzymology by multimodular nonribosomal peptide synthetases: the thioesterase domain of E. coli EntF catalyzes both elongation and cyclolactonization.

BACKGROUND: EntF is a 142 kDa four domain (condensation-adenylation-peptidyl carrier protein-thioesterase) nonribosomal peptide synthetase (NRPS) enzyme that assembles the Escherichia coli N-acyl-serine trilactone siderophore enterobactin from serine, dihydroxybenzoate (DHB) and ATP with three other enzymes (EntB, EntD and EntE). To assess how EntF forms three ester linkages and cyclotrimerizes the covalent acyl enzyme DHB-Ser-S-PCP (peptidyl carrier protein) intermediate, we mutated residues of the proposed catalytic Ser-His-Asp triad of the thioesterase (TE) domain. RESULTS: The Ser1138-->Cys mutant (kcat decreased 1000-fold compared with wild-type EntF) releases both enterobactin (75%) and linear (DHB-Ser)2 dimer (25%) as products. The His 1271-->Ala mutant (kcat decreased 10,000-fold compared with wild-type EntF) releases only enterobactin, but accumulates both DHB-Ser-O-TE and (DHB-Ser)2-O-TE acyl enzyme intermediates. Electrospray ionization and Fourier transform mass spectrometry of proteolytic digests were used to analyze the intermediates. CONCLUSIONS: These results establish that the TE domain of EntF is both a cyclotrimerizing lactone synthetase and an elongation catalyst for ester-bond formation between covalently tethered DHB-Ser moieties, a new function for chain-termination TE domains found at the carboxyl termini of multimodular NRPSs and polyketide synthases.     

The structure of a model intermediate for the nickel-catalyzed cyclodimerization of allene

The stoichiometric reaction between allene, zerovalent nickel and a chelating diphosphane leads to the formation of a bis-methylenenickelacyclopentane derivative whose structure has been established by X-ray crystallography.     

Concerning the product of [2 + 2] cyclodimerization of 9-allenylcarbazole

The isomerization of 9-propargylcarbazole in alcoholic alkali leads to the product of dimerization of 9-allenylcarbazole, 1,2-bis(9-carbazolylmethylene)cyclobutane, the structure of which was established by X-ray diffraction analysis.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1652–1661, November, 2004.     

Biosynthesis of vitamin B12: the multi-enzyme synthesis of precorrin-4 and factor IV

Background: In order to study the biosynthesis of vitamin B₁₂, it is necessary to produce various intermediates along the biosynthetic pathway by enzymic methods. Recently, information on the organisation of the biosynthetic pathway has permitted the selection of the set of enzymes needed to biosynthesise any specific identified intermediate. The aim of the present work was to use recombinant enzymes in reconstituted multi-enzyme systems to biosynthesise particular intermediates.Results: The products of the cobG and cobJ genes from Pseudomonas denitrificans were expressed heterologously in Escherichia coli to afford good levels of activity of the corresponding enzymes, CobG and CobJ. Aerobic incubation of precorrin-3A with the CobG enzyme alone yielded precorrin-3B. When CobJ and S-adenosyl-l-methionine were included in the incubation, the product was precorrin-4. Both precorrin-3B and precorrin-4 are known precursors of vitamin B₁₂ and their availability has allowed new mechanistic studies of enzymic transformations.Conclusions: Our results show that the expression of the CobG and CobJ enzymes has been successful, thus facilitating the biosynthesis of two precursors of vitamin B₁₂. This lays the foundation for the structure determination of CobG and CobJ as well as future enzymic experiments focusing on later steps of vitamin B₁₂ biosynthesis.     

CmlI is an N-oxygenase in the biosynthesis of chloramphenicol

The N-oxygenation of an amine group is one of the steps in the biosynthesis of the antibiotic chloramphenicol. The non-heme di-iron enzyme CmlI was identified as the enzyme catalyzing this reaction through bioinformatics studies and reconstitution of enzymatic activity. In vitro reconstitution was achieved using phenazine methosulfate and NADH as electron mediators, while in vivo activity was demonstrated in Escherichia coli using two substrates. Kinetic analysis showed a biphasic behavior of the enzyme. Oxidized hydroxylamine and nitroso compounds in the reaction were detected both in vitro and in vivo based on LC–MS. The active site metal was confirmed to be iron based on a ferrozine assay. These findings provide new insights into the biosynthesis of chloramphenicol and could lead to further development of CmlI as a useful biocatalyst.     

The photochemical [4+4] cyclodimerization of 2-pyrazinone in the solid state

Irradiation of 1-methyl-5,6-diphenyl-2-pyrazinone (Ia) in the solid state gave the [4+4] anti dimer (II) in 100% yield, while (Ia) in a solution phase was inert upon irradiation.     

Assembly line termination in cylindrocyclophane biosynthesis: discovery of an editing type II thioesterase domain in a type I polyketide synthase

The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering.