Structure revision of cryptosporioptides and determination of the genetic basis for dimeric xanthone biosynthesis in fungi

Three novel dimeric xanthones, cryptosporioptides A-C were isolated from Cryptosporiopsis sp. 8999 and their structures elucidated. Methylation of cryptosporioptide A gave a methyl ester with identical NMR data to cryptosporioptide, a compound previously reported to have been isolated from the same fungus. However, HRMS analysis revealed that cryptosporioptide is a symmetrical dimer, not a monomer as previously proposed, and the revised structure was elucidated by extensive NMR analysis. The genome of Cryptosporiopsis sp. 8999 was sequenced and the dimeric xanthone (dmx) biosynthetic gene cluster responsible for the production of the cryptosporioptides was identified. Gene disruption experiments identified a gene (dmxR5) encoding a cytochrome P450 oxygenase as being responsible for the dimerisation step late in the biosynthetic pathway. Disruption of dmxR5 led to the isolation of novel monomeric xanthones. Cryptosporioptide B and C feature an unusual ethylmalonate subunit: a hrPKS and acyl CoA carboxylase are responsible for its formation. Bioinformatic analysis of the genomes of several fungi producing related xanthones, e.g. the widely occurring ergochromes, and related metabolites allows detailed annotation of the biosynthetic genes, and a rational overall biosynthetic scheme for the production of fungal dimeric xanthones to be proposed.

The Challenging in silico Description of Carbon Monoxide Oxidation as Catalyzed by Molybdenum-Copper CO Dehydrogenase

Carbon monoxide (CO) is a highly toxic gas to many living organisms. However, some microorganisms are able to use this molecule as the sole source of carbon and energy. Soil bacteria such as the aerobic Oligotropha carboxidovorans are responsible for the annual removal of about 2x108 tons of CO from the atmosphere. Detoxification through oxidation of CO to CO2 is enabled by the MoCu-dependent CO-dehydrogenase enzyme (MoCu-CODH) which-differently from other enzyme classes with similar function-retains its catalytic activity in the presence of atmospheric O2. In the last few years, targeted advancements have been described in the field of bioengineering and biomimetics, which is functional for future technological exploitation of the catalytic properties of MoCu-CODH and for the reproduction of its reactivity in synthetic complexes. Notably, a growing interest for the quantum chemical investigation of this enzyme has recently also emerged. This mini-review compiles the current knowledge of the MoCu-CODH catalytic cycle, with a specific focus on the outcomes of theoretical studies on this enzyme class. Rather controversial aspects from different theoretical studies will be highlighted, thus illustrating the challenges posed by this system as far as the application of density functional theory and hybrid quantum-classical methods are concerned.

Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations

The apparently simple dihydrogen formation from protons and electrons (2H⁺ + 2e^- ⇄ H₂) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H₂ as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni-B and Ni-A states of the [NiFe]-hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni-B and Ni-A. However, this process is sufficient to activate only the Ni-B state. H₂ binding to the active site is required to convert Ni-A to the active Ni-SI_a state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni-SI_r and Ni-SU species, formed respectively from the one-electron reduction of Ni-B and Ni-A. Ni-SI_r, depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni-SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni-A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H₂O and H₂ binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni-B and Ni-A states.

C-Myc Deregulation is Involved in Melphalan Resistance of Multiple Myeloma: Role of PDGF-BB

Oncogenes are important regulators of cancer growth and progression and their action may be modulated by proteins of the growth factor family, such as angiogenic cytokines, known to be strongly involved in neoplastic evolution. Reciprocal interactions between oncogenes and angiogenic modulators may represent, in haematological neoplasms, including multiple myeloma (MM), a possible mechanism of drug resistance. The aim of this work is to investigate in vitro and in vivo whether or not c-myc deregulation is involved in the melphalan resistance elicited by myeloma patients and consequently to clarify the role of the angiogenic factor PDGF-BB in modulating c-myc protein expression. Fifty-one MM patients on chemotherapy with melphalan were analyzed for structural alterations of the c-myc gene, c-Myc protein expression, as well as for serum PDGF-BB release. For the in vitro study, two M14-derived established cell clones, differing for the c-Myc protein expression (c-Myc low -expressing or constitutively expressing clones) were used. Our results show that PDGF-BB is able to up-regulate Myc expression and reduce melphalan sensitivity of tumor cell clones, constitutively expressing c-myc gene product. In addition, down-regulation of c-Myc protein induces the expression of PDGF-β receptor molecules and reduces PDGF-BB release. In agreement with these results, in vivo data show that melphalan-resistant MM patients present overexpressed c-Myc protein and higher serum PDGF-β receptor levels compared to minor responding patients.

The epigenetic reader SntB regulates secondary metabolism, development and global histone modifications in Aspergillus flavus

Due to the role, both beneficial and harmful, that fungal secondary metabolites play in society, the study of their regulation is of great importance. Genes for any one secondary metabolite are contiguously arranged in a biosynthetic gene cluster (BGC) and subject to regulation through the remodeling of chromatin. Histone modifying enzymes can place or remove post translational modifications (PTM) on histone tails which influences how tight or relaxed the chromatin is, impacting transcription of BGCs. In a recent forward genetic screen, the epigenetic reader SntB was identified as a transcriptional regulator of the sterigmatocystin BGC in A. nidulans, and regulated the related metabolite aflatoxin in A. flavus. In this study we investigate the role of SntB in the plant pathogen A. flavus by analyzing both ΔsntB and overexpression sntB genetic mutants. Deletion of sntB increased global levels of H3K9K14 acetylation and impaired several developmental processes including sclerotia formation, heterokaryon compatibility, secondary metabolite synthesis, and ability to colonize host seeds; in contrast the overexpression strain displayed fewer phenotypes. ΔsntB developmental phenotypes were linked with SntB regulation of NosA, a transcription factor regulating the A. flavus cell fusion cascade.

Targeting Amyloid Aggregation: An Overview of Strategies and Mechanisms

Amyloids result from the aggregation of a set of diverse proteins, due to either specific mutations or promoting intra- or extra-cellular conditions. Structurally, they are rich in intermolecular β-sheets and are the causative agents of several diseases, both neurodegenerative and systemic. It is believed that the most toxic species are small aggregates, referred to as oligomers, rather than the final fibrillar assemblies. Their mechanisms of toxicity are mostly mediated by aberrant interactions with the cell membranes, with resulting derangement of membrane-related functions. Much effort is being exerted in the search for natural antiamyloid agents, and/or in the development of synthetic molecules. Actually, it is well documented that the prevention of amyloid aggregation results in several cytoprotective effects. Here, we portray the state of the art in the field. Several natural compounds are effective antiamyloid agents, notably tetracyclines and polyphenols. They are generally non-specific, as documented by their partially overlapping mechanisms and the capability to interfere with the aggregation of several unrelated proteins. Among rationally designed molecules, we mention the prominent examples of β-breakers peptides, whole antibodies and fragments thereof, and the special case of drugs with contrasting transthyretin aggregation. In this framework, we stress the pivotal role of the computational approaches. When combined with biophysical methods, in several cases they have helped clarify in detail the protein/drug modes of interaction, which makes it plausible that more effective drugs will be developed in the future.

Cyclophosphamide and Iphosphamide against Lewis Lung Carcinoma: Evaluation of Toxic and Therapeutic Effects

In the present report, investigations have been carried out to evaluate toxic and therapeutic effects of cyclophosphamide vs its isomer iphosphamide. Cytostatic action of the 2 drugs was assayed on the murine Lewis lung carcinoma (3LL). It has been observed that iphosphamide is less toxic as compared to cyclophosphamide [Formula: see text]; on the other hand, to reach the same therapeutic effectiveness on 3LL, an iphosphamide dose 1.6 - 2 times higher than that of its parent compound is necessary.

3D-Conformal Radiation Therapy in Prostate Cancer. Technical Considerations after 5 Years of Experience and 334 Patients Treated at the Istituto Europeo Di Oncologia of Milan, Italy

Aims and Background

To report the technique of 3D-conformal radiation therapy (3D-CRT) currently used at our Institute for the treatment of prostate cancer with a curative intent. A critical review of the technical aspects of the technique is provided.

Methods and Study Design

Between December 1995 and October 2000, 334 patients with biopsy-proven adenocarcinoma of the prostate were treated with 3D-CRT. All patients were treated in a prone position with 15 MV X-ray beams and a 6-field technique for all but 20 patients, who were treated with a 3-field technique. Patients were simulated with the rectum and bladder empty. To ensure reproducible positioning, custom-made polyurethane foam or thermoplastic casts were produced for each patient. Subsequently, consecutive CT scan slices were obtained. The clinical target volume and critical organs (rectum and bladder) were identified on each CT slice. The beam's eye view technique was used to spatially display these structures, and the treatment portals were manually shaped based on the images obtained. The beam apertures were initially realized by conventional Cerrobend blocks (48 patients), which were replaced in October 1997 by a computer-driven multi-leaf collimator. The total target dose prescribed at the ICRU point is 76 Gy, delivered in 38 fractions and 54 days. The seminal vesicles are excluded at 70 Gy. Dose-volume histograms were obtained for all patients. If more than 30% of the bladder and/or more than 20% of the rectum receive >95% of the prescribed total dose, the treatment plan is judged as unsatisfactory and is adjusted. The dose-volume histogram can be improved by changing the beam's arrangement and/or weights or by introducing or modifying the wedge filters.

Conclusions

3D-CRT in prostate cancer patients is a highly sophisticated and time-consuming method of dose delivery. Important technical issues remain to be clarified.

Cell Proliferation Kinetics of the Intramuscularly Implanted Lewis Lung Carcinoma

The growth kinetics of the Lewis lung carcinoma tumor was studied. The main proliferative parameters of an early stage of the growth (8th day after tumor implantation) were derived from the analysis of the growth curve and the fraction of labeled mitoses (FLM curve). The occurrence of proliferative changes due to the transplantation was confirmed. The main variations observed concern a shortening of the cell cycle time, a prolongation of the S phase duration and an increase in cell loss. A critical analysis of the results of this preliminary study is reported.

Interaction of the H-Cluster of FeFe Hydrogenase with Halides

FeFe hydrogenases catalyze H₂ oxidation and production using an "H-cluster", where two Fe ions are bound by an aza-dithiolate (adt) ligand. Various hypotheses have been proposed (by us and others) to explain that the enzyme reversibly inactivates under oxidizing, anaerobic conditions: intramolecular binding of the N atom of adt, formation of the so-called "Hox/inact" state or nonproductive binding of H₂ to isomers of the H-cluster. Here, we show that none of the above explains the new finding that the anaerobic, oxidative, H₂-dependent reversible inactivation is strictly dependent on the presence of Cl^- or Br^-. We provide experimental evidence that chloride uncompetitively inhibits the enzyme: it reversibly binds to catalytic intermediates of H₂ oxidation (but not to the resting "Hox" state), after which oxidation locks the active site into a stable, saturated, inactive form, the structure of which is proposed here based on DFT calculations. The halides interact with the amine group of the H-cluster but do not directly bind to iron. It should be possible to stabilize the inhibited state in amounts compatible with spectroscopic investigations to explore further this unexpected reactivity of the H-cluster of hydrogenase.

The cycloaspeptides: uncovering a new model for methylated nonribosomal peptide biosynthesis

The cycloaspeptide gene cluster includes a pathway-specific N-methyl transferase. Its disruption allowed incorporation of N-methylated amino acids provided in the culture medium, allowing efficient production of cycloaspeptide E and novel related products.

The cycloaspeptides are bioactive pentapeptides produced by various filamentous fungi, which have garnered interest from the agricultural industry due to the reported insecticidal activity of the minor metabolite, cycloaspeptide E. Genome sequencing, bioinformatics and heterologous expression confirmed that the cycloaspeptide gene cluster contains a minimal 5-module nonribosomal peptide synthetase (NRPS) and a new type of trans-acting N-methyltransferase (N-MeT). Deletion of the N-MeT encoding gene and subsequent feeding studies determined that two modules of the NRPS preferentially accept and incorporate N-methylated amino acids. This discovery allowed the development of a system with unprecedented control over substrate supply and thus output, both increasing yields of specific metabolites and allowing the production of novel fluorinated analogues. Furthermore, the biosynthetic pathway to ditryptophenaline, another fungal nonribosomal peptide, was shown to be similar, in that methylated phenylalanine is accepted by the ditryptophenaline NRPS. Again, this allowed the directed biosynthesis of a fluorinated analogue, through the feeding of a mutant strain. These discoveries represent a new paradigm for the production of N-methylated cyclic peptides via the selective incorporation of N-methylated free amino acids.

Theoretical investigation of aerobic and anaerobic oxidative inactivation of the [NiFe]-hydrogenase active site

The extraordinary capability of [NiFe]-hydrogenases to catalyse the reversible interconversion of protons and electrons into dihydrogen (H₂) has stimulated numerous experimental and theoretical studies addressing the direct utilization of these enzymes in H₂ production processes.