Aureolic acids: similar antibiotics with different biosynthetic gene clusters

In this issue of Chemistry & Biology, Méndez and colleagues describe the sequence and organization of the chromomycin gene cluster. Unexpectedly, the arrangement is starkly different from the mithramycin biosynthetic cluster, despite similarity in the individual genes and the near identical structures of the two antibiotic aureolic acids.     

Characterization of the secondary metabolite biosynthetic gene clusters in archaea

Secondary metabolites are a range of bioactive compounds yielded by bacteria, fungi and plants, etc. The published archaea genomic data provide the opportunity for efficient identification of secondary metabolite biosynthetic gene clusters (BGCs) by genome mining. However, the study of secondary metabolites in archaea is still rare. By using the antiSMASH, we found two main putative secondary metabolite BGCs, bacteriocin and terpene in 203 Archaea genomes. Compared with the genomes of Euryarchaeota that usually lives in less complexity of environment, the genomes of Crenarchaeota usually contained more abundant bacteriocin. In these archaea genomes, we also found the positive correlation between the abundance of bacteriocin and the abundance of CRISPR spacer, suggesting the bacteriocin might be a crucial component of the innate immune system that defense the microbe living in the common environment. The structure analysis of the bacteriocin gene clusters gave a clue that the assisted genes located at the edge of clusters evolved faster than the core biosynthetic genes. To the best of our knowledge, we are the first to systematically explore the distribution of secondary metabolites in archaea, and the investigation of the relationship between BGC and CRISPR spacer expands our understanding of the evolutionary dynamic of these functional molecules.     

Genome-wide high-throughput mining of natural-product biosynthetic gene clusters by phage display

We have developed a phage-display method for high-throughput mining of bacterial gene clusters encoding the natural-product biosynthetic enzymes, polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). This method uses the phosphopantetheinyl transferase activity of Sfp to specifically biotinylate NRPS and PKS carrier-protein domains expressed from a library of random genome fragments fused to a gene encoding a phage coat protein. Subsequently, the biotinylated phages are enriched through selection on streptavidin-coated plates. Using this method, we isolated phage clones from the multiple NRPS and PKS gene clusters encoded in the genomes of Bacillus subtilis and Myxococcus xanthus. Due to the rapid and unambiguous identification of carrier domains, this method will provide an efficient tool for high-throughput cloning of NRPS and PKS gene clusters from many individual bacterial genomes and multigenome environmental DNA.     

The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters

With the increasing number of genomes sequenced and available in the public domain, a large number of orphan gene clusters, for which the encoded natural product is unknown, have been identified. These orphan gene clusters represent a tremendous source of novel and possibly bioactive compounds. Here, we describe a "genomisotopic approach," which employs a combination of genomic sequence analysis and isotope-guided fractionation to identify unknown compounds synthesized from orphan gene clusters containing nonribosomal peptide synthetases. Analysis of the Pseudomonas fluorescens Pf-5 genome led to the identification of an orphan gene cluster predicted to code for the biosynthesis of a lipopeptide natural product. Application of the genomisotopic approach to isolate the product of this gene cluster resulted in the discovery of orfamide A, founder of a group of bioactive cyclic lipopeptides.     

Stability and structure of rare-gas ionic clusters using density functional methods: A study of helium clusters

Several modelings of exchange and correlation forces which can be carried out using density functional theory (DFT) methods have been analyzed to study their efficiency and reliability when evaluating possible competing structures of helium ionic clusters of increasing size. This study examines He_n⁺systems with n from 1 to 7 and compares the present calculations with earlier evaluations that used more conventional, and more computationally intensive, methods with configuration interaction (CI) approaches. The present results indicate that it is indeed possible to strike a fruitful balance between reduction of computational times and quality of the ensuing structural information. © 1996 John Wiley & Sons, Inc.     

Small ScCn cyclic clusters: a density functional study of their structure and stability

A theoretical study of the ScCn, ScCn+, and ScCn- (n = 1-10) cyclic clusters has been carried out employing the B3LYP density functional method. Predictions for several molecular properties that could help in their possible experimental characterization, such as equilibrium geometries, electronic structures, dipole moments, and vibrational frequencies, are reported. All ScCn cyclic clusters are predicted to have doublet ground states. For cationic clusters the ground state is alternate between singlets (n-even species) and triplets (n-odd members). In the case of anionic clusters the singlet-triplet separation is relatively small, with the singlets being favored in most cases. In general, even-odd parity effects are also observed for different properties, such as incremental binding energies, ionization energies, and electron affinities. For all neutral, cationic, and anionic clusters it is found that cyclic species are more stable than their open-chain counterparts. Therefore, cyclic structures are the most interesting possible targets for an experimental search of scandium-doped carbon clusters.     

Minor alkaloids of Aspidosperma subincanum mart.: isolation, structure proof and synthesis of 1,2-dihydro-ellipticine, 1,2-dihydro-ellipticine methonitrate and ellipticine methonitrate

Three alkaloids named in the title were isolated from the Peruvian plant “Quillo-bordon.” The structures assigned were confirmed by partial syntheses.     

Cloning, sequencing, and functional analysis of the biosynthetic gene cluster of macrolactam antibiotic vicenistatin in Streptomyces halstedii

Vicenistatin, an antitumor antibiotic isolated from Streptomyces halstedii, is a unique 20-membered macrocyclic lactam with a novel aminosugar vicenisamine. The vicenistatin biosynthetic gene cluster (vin) spanning approximately 64 kbp was cloned and sequenced. The cluster contains putative genes for the aglycon biosynthesis including four modular polyketide synthases (PKSs), glutamate mutase, acyl CoA-ligase, and AMP-ligase. Also found in the cluster are genes of NDP-hexose 4,6-dehydratase and aminotransferase for vicenisamine biosynthesis. For the functional confirmation of the cluster, a putative glycosyltransferase gene product, VinC, was heterologously expressed, and the vicenisamine transfer reaction to the aglycon was chemically proved. A unique feature of the vicenistatin PKS is that the loading module contains only an acyl carrier protein domain, in contrast to other known PKS-loading modules containing certain activation domains. Activation of the starter acyl group by separate polypeptides is postulated as well.     

Binary clusters AuPt and Au6Pt: structure and reactivity within density functional theory

Within density functional theory with the general gradient approximation for the exchange and correlation, the bimetallic clusters AuPt and Au(6)Pt have been studied for their structure and reactivity. The bond strength of AuPt lies between those of Au(2) and Pt(2), and it is closer to that of Au(2). The Pt atom is the reactive center in both AuPt and AuPt(+) according to electronic structure analysis. AuPt(+) is more stable than AuPt. Au(6)Pt prefers electronic states with low multiplicity. The most stable conformation of Au(6)Pt is a singlet and has quasi-planar hexagonal frame with Pt lying at the hexagonal center. The doping of Pt in Au cluster enhances the chemical regioselectivity of the Au cluster. The Pt atom essentially serves as electron donor and the Au atoms bonded to the Pt atom acts as electron acceptor in Au(6)Pt. The lowest triplet of edge-capped rhombus Au(6)Pt clusters is readily accessible with very small singlet-triplet energy gap (0.32 eV). O(2) prefers to adsorb on Au and CO prefers to adsorb on Pt. O(2) and CO have stronger adsorption on AuPt than they do on Au(6)Pt. CO has a much stronger adsorption on AuPt bimetallic cluster than O(2) does. The adsorption of CO on Pt modifies the geometry of AuPt bimetallic clusters.     

Electronic structure of oxide, peroxide, and superoxide clusters of the 3d elements: a comparative density functional study

The 3d-element transition metal dioxide MO(2), peroxide M(O(2)), and superoxide MOO clusters (M=Sc-Zn), are studied by density functional theory with the B1LYP functional. The reliability of the methods and basis sets employed was tested by a reinvestigation of the monoxides, for which a database of experimental data is available. The global minima on the M+O(2) potential energy surfaces correspond to dioxide structure, the only exception being CuOO, with a superoxide structure. All Zn dioxygen clusters are thermodynamically unstable-their ground states lie higher than the dissociation limit to Zn+O(2). Our calculations are in favor of the high-spin configurations for the FeO(2), CoO(2), and NiO(2) ground states, which are still a subject of extensive theoretical and experimental studies. These assignments are confirmed by the coupled-cluster method, CCSD(T), except for NiO(2). Based on the existence of a stable NiO(2) monoanion in a (4)B(1) state, however, it can be concluded that NiO(2) in its (5)A(1) state should also be stable. The vibrational frequencies are calculated for clusters entrapped in the cubic cell of solid Ar matrix and compared with those obtained for gas-phase clusters. The matrix has no influence on the vibrations of the monoxides and most of the dioxides; however, Co and Ni-dioxoclusters interact strongly with the atoms from the noble gas matrix. The most intense frequencies in the IR spectra are shifted to lower energies and the ordering of the low-lying electronic states by stability is also reversed. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides. The terminal oxygen atom in superoxides is more nucleophilic than its M-bonded oxygen atom, though charge distribution analysis predicts a smaller negative charge on the terminal oxygen. TiO(2) is the only dioxide in which nucleophilic character in the vicinity of the metal cation is induced.     

Energetics, structure, and electron detachment spectra of calcium and zinc neutral and anion clusters: a density functional theory study

A hybrid density functional approach with very large basis sets was used for studying Ca2 through Ca19 and Zn3 through Zn11 neutral clusters and their cluster anions. Energetics, structure, and vibrational analysis of all these neutral clusters and cluster anions are reported. The calculated electron affinities are in excellent agreement with experiment displaying a characteristic kink at Ca10 and Zn10. This kink occurs because the 10-atom neutral cluster is very stable whereas the cluster anion is not. Additionally, the electron detachment binding energies (BEs) up to Ca6(-) and Zn6(-) were identified by analyzing the ground and excited states of the cluster anions and of their corresponding size neutral clusters. The theoretical BE is in very good agreement with experiment for both calcium and zinc cluster anions. The three main peaks in the spectrum correspond to BEs from the ground state of the cluster anion (doublet) to the ground state of the neutral cluster (singlet) and to the first triplet and quintet excited states of the neutral cluster. The calculated energy gap from the lowest BE peak to the second peak is in excellent agreement with experiment. The calculation reproduces very well the energy gap observed in Ca4(-) and Zn4(-), which is larger than those for other sizes and is indicative of the strong stability of the anion and neutral tetramers.     

Silicon clusters: chemistry and structure

The chemical reactions of size selected silicon cluster ions (containing up to 70 atoms) have been studied with a number of different reagents using injected ion drift tube techniques. Both kinetic and equilibrium measurements have been performed as a function of temperature, and the influence of cluster annealing on chemical reactivity explored. Unlike metal clusters, where bulk behavior appears to be approached with around 30 atoms, large silicon clusters (n up to 70) are much less reactive than bulk silicon surfaces. These results suggest that the clusters in the size range examined here are not small crystals of bulk silicon, but have compact, high coordination number structures with few dangling bonds.     

2-Substituted-3,7-dinitro-11-oxatricycloundec-9-ene: an approach towards the synthesis of Ergot alkaloids

A simple and versatile method for the preparation of various ergoline or secoergoline skeleton, using 2-substituted-3,7-dinitro-11-oxatricycloundec-9-ene as key intermediates, is described. The key step involves an IMDAF reaction with an excellent stereocontrol. This novel synthetic route provides new cycloadducts as useful scaffolds for Ergot alkaloids synthesis.     

Two separate gene clusters encode the biosynthetic pathway for the meroterpenoids austinol and dehydroaustinol in Aspergillus nidulans

Meroterpenoids are a class of fungal natural products that are produced from polyketide and terpenoid precursors. An understanding of meroterpenoid biosynthesis at the genetic level should facilitate engineering of second-generation molecules and increasing production of first-generation compounds. The filamentous fungus Aspergillus nidulans has previously been found to produce two meroterpenoids, austinol and dehydroaustinol. Using targeted deletions that we created, we have determined that, surprisingly, two separate gene clusters are required for meroterpenoid biosynthesis. One is a cluster of four genes including a polyketide synthase gene, ausA. The second is a cluster of 10 additional genes including a prenyltransferase gene, ausN, located on a separate chromosome. Chemical analysis of mutant extracts enabled us to isolate 3,5-dimethylorsellinic acid and 10 additional meroterpenoids that are either intermediates or shunt products from the biosynthetic pathway. Six of them were identified as novel meroterpenoids in this study. Our data, in aggregate, allow us to propose a complete biosynthetic pathway for the A. nidulans meroterpenoids.