Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.     

David and Goliath: chemical perturbation of eukaryotes by bacteria

Environmental microbes produce biologically active small molecules that have been mined extensively as antibiotics and a smaller number of drugs that act on eukaryotic cells. It is known that there are additional bioactives to be discovered from this source. While the discovery of new antibiotics is challenged by the frequent discovery of known compounds, we contend that the eukaryote-active compounds may be less saturated. Indeed, despite there being far fewer eukaryotic-active natural products these molecules interact with a far richer diversity of molecular and cellular targets.     

Optical-fiber bundles

Optical-fiber bundles have been employed as a versatile substrate for the fabrication of high-density microwell arrays. In this minireview, we discuss the application of optical-fiber-bundle arrays for a variety of biological problems. For genomics studies and microbial pathogen detection, individual beads have been functionalized with DNA probes and then loaded into the microwells. In addition, beads differentially responsive to vapors have been employed in an artificial olfaction system. Microwell arrays have also been loaded with living cells to monitor their individual response to biologically active compounds over long periods. Finally, the microwells have been sealed to enclose single enzyme molecules that can be used to measure individual molecule catalytic activity.     

Eliciting secondary metabolism in plant cell cultures

Plant cell cultures are potentially rich sources of valuable pharmaceuticals and other biologically active phytochemicals, but relatively few cultures synthesize secondary compounds over extended periods in amounts comparable to those found in the whole plant. Frequently, no secondary metabolites characteristic of the intact plant are produced. So far, the manipulation of culture media, culture conditions and phytohormone levels have, in general, failed to permit commercial production of those phytochemicals useful in medicine and industry. This almost certainly reflects the lack of understanding of basic secondary metabolic regulation in cultured plant cells.

Microbial insult can induce antibiotic phytochemical synthesis in cultured plant cells: the microbial molecules which stimulate synthesis have been called ‘elicitors’. Increased synthesis of secondary products in response to elicitation of various types appear to be the general response of cultured cells. This paper illustrates the immense biotechnological potential of plant cell culture—‘elicitor’ (inducer) interactions to the large scale production of secondary metabolites, and suggests several lines of enquiry that remain to be authoritatively treated.     

成像质谱在微生物代谢产物研究中的应用

微生物代谢产物的结构和功能多样,对相邻微生物和环境会产生重要影响。传统的天然产物分离方法不能系统全面地监测单一或混合微生物样品中代谢物的合成和释放模式。成像质谱能够同时可视化观察从单一微生物菌落到复杂微生物群落的多个代谢产物的时空分布,可以用于发现重要的生物活性分子,观察微生物菌落的代谢交流,以及跟踪微生物之间相互竞争过程中代谢物的修饰等方面的研究。本文综述了成像质谱在微生物代谢产物研究中的最新进展,展望了该技术的应用前景。     

Small molecule intercalation with double stranded DNA: implications for normal gene regulation and for predicting the biological efficacy and genotoxicity of drugs and other chemicals

The binding of small molecules to double stranded DNA including intercalation between base pairs has been a topic of research for over 40 years. For the most part, however, intercalation has been of marginal interest given the prevailing notion that binding of small molecules to protein receptors is largely responsible for governing biological function. This picture is now changing with the discovery of nuclear enzymes, e.g. topoisomerases that modulate intercalation of various compounds including certain antitumor drugs and genotoxins. While intercalators are classically flat, aromatic structures that can easily insert between base pairs, our laboratories reported in 1977 that a number of biologically active compounds with greater molecular thickness, e.g. steroid hormones, could fit stereospecifically between base pairs. The hypothesis was advanced that intercalation was a salient feature of the action of gene regulatory molecules. Two parallel lines of research were pursued: (1) development of technology to employ intercalation in the design of safe and effective chemicals, e.g. pharmaceuticals, nutraceuticals, agricultural chemicals; (2) exploration of intercalation in the mode of action of nuclear receptor proteins. Computer modeling demonstrated that degree of fit of certain small molecules into DNA intercalation sites correlated with degree of biological activity but not with strength of receptor binding. These findings led to computational tools including pharmacophores and search engines to design new drug candidates by predicting desirable and undesirable activities. The specific sequences in DNA into which ligands best intercalated were later found in the consensus sequences of genes activated by nuclear receptors implying intercalation was central to their mode of action. Recently, the orientation of ligands bound to nuclear receptors was found to match closely the spatial locations of ligands derived from intercalation into unwound gene sequences suggesting that nuclear receptors may be guiding ligands to DNA with remarkable precision. Based upon multiple lines of experimental evidence, we suggest that intercalation in double stranded DNA is a ubiquitous, natural process and a salient feature of the regulation of genes. If double stranded DNA is proven to be the ultimate target of genomic drug action, intercalation will emerge as a cornerstone of the future discovery of safe and effective pharmaceuticals.     

<Emphasis Type="Italic">Streptomyces</Emphasis> metabolites in divergent microbial interactions

Streptomyces and related bacteria produce a wide variety of secondary metabolites. Of these, many compounds have industrial applications, but the question of why this group of microorganism produces such various kinds of biologically active substances has not yet been clearly answered. Here, we overview the results from our studies on the novel function and role of Streptomyces metabolites. The diverged action of negative and positive influences onto the physiology of various microorganisms infers the occurrence of complex microbial interactions due to the effect of small molecules produced by Streptomyces. The interactions may serve as a basis for the constitution of biological community.     

The logic of biologically active small molecules: amazing ability of microorganisms*

In this review article, I will outline my way of thinking about biologically active small molecules. The structure of liposidomycin B from Streptomyces species resulted in my initial sense that a structure tells its function. A biologically active small molecule may save directly or indirectly a number of people. Even if the molecule has not been used as a therapeutic agent, it can be used as a useful chemical probe for dissecting a living cell into different biochemical pieces. Such biologically active small molecules derived from microorganisms have been primarily found in cultivable microorganisms that make up only 1% of total microbes in nature. Discovery of novel growth factors, zincmethylphyrin, zinc coproporphyrin, and coproporphyrin enabled laboratory cultivation of previously uncultured Leucobacter sp. These findings might expand the possibility for further discovery of novel therapeutic agents or chemical probes.     

Antimicrobial compounds from the excretions of surgical maggots, Lucilia sericata (Meigen) (Diptera, Calliphoridae)

Maggots of Lucilia sericata are widely used in the therapy of infected wounds and skin ulcers. Antimicrobial materials released by the insects during their feeding period in order to suppress microbial competitors and potential pathogens play the key role both in the maggots’ survival in their natural habitats (animal corpses) and their therapeutic efficacy. Although the antimicrobial activity of the maggots’ excretion was demonstrated about a hundred years ago, little is known about the nature of its active compounds. We studied the structural characteristics and antimicrobial activities of the compounds released by L. sericata maggots into the environment. To isolate the compounds, excretion was collected from the culture of actively feeding last instar larvae, active compounds were purified using a combination of liquid chromatography and antibacterial growth inhibition assay and characterized by mass spectrometry. Two groups of antibacterial compounds were isolated from the excretion: polypeptides with molecular masses ranging from 6466 to 9025 Da and small molecules with molecular masses ranging from 130 to 700 Da. The polypeptides characterized by the masses of 8882 and 9025 Da and showing selective activity against Gram-negative bacteria correspond well to diptericins, antimicrobial peptides previously found in the hemolymph of Calliphoridae maggots and known to be part of immune response to bacterial pathogens. Other high-molecular compounds with masses 6466, 6633, 5772, and 8631 Da have no clear analogs among antimicrobial peptides present in the hemolymph. The nature of small molecules present in the excretion awaits further study. Thus, the diversity of antimicrobial compounds discovered in Lucilia excretion demonstrates a sophisticated strategy that helps the maggots to fight bacteria and other microorganisms settling their environment. The strategy combines secretion of a set of antibacterial peptides involved in insect immune response as well as molecules which function outside the host organism.     

Double-stranded DNA liquid-crystalline dispersions as biosensing units

Three different approaches to constructing biosensing units based on double-stranded (ds) DNA molecules, capable of detecting various biologically active compounds, are considered. The first approach is based on the abnormal optical activity of the liquid-crystalline dispersion formed from ds DNA molecules, modified by relevant physical factors or treated with biologically active compounds. The second one is based on the abnormal optical activity of the liquid-crystalline dispersions formed first from the ds DNA and then treated with coloured biologically active compounds. The third one is based on the abnormal optical activity, specific to particles of the liquid-crystalline dispersions, where the neighbouring DNA molecules are crosslinked by artificial polymeric bridges. These approaches permit the detection of biologically relevant compounds of various origins.     

Predicting the unpredictable: Recent structure–activity studies on peptide-based macrocycles

Heterocycle-containing macrocycles are an emerging class of molecules that have therapeutic efficacy. Many biologically active natural products that have interesting biological properties fall into this class of molecules. The highly specific and selective biological activity is often attributed to the unique conformation of these macrocycles, which is affected by the elements of the macrocycles as well as its surroundings in biological systems. In this review, the structure–activity relationship studies of several recently developed biologically active heterocycle-containing macrocycles have been discussed in order to facilitate an understanding on how unpredictable structures can be controlled.     

Rare actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway: isolation, diversity and biological activity

Actinomycete bacteria produce a wide variety of secondary metabolites with diverse biological activities, some of which have been developed for human medicine. Rare actinomycetes are promising sources in search for new drugs, and their potential for producing biologically active molecules is poorly studied. In this work, we have investigated the diversity of actinomycetes in the shallow water sediments of the Trondheim fjord (Norway). Due to the use of different selective isolation methods, an unexpected variety of actinomycete genera was isolated. Although the predominant genera were clearly Streptomyces and Micromonospora, representatives of Actinocorallia, Actinomadura, Knoellia, Glycomyces, Nocardia, Nocardiopsis, Nonomuraea, Pseudonocardia, Rhodococcus and Streptosporangium genera were isolated as well. To our knowledge, this is the first report describing isolation of Knoellia and Glycomyces species from the marine environment. 35 selected actinomycete isolates were characterized by 16S rDNA sequencing, and were shown to represent strains from 11 different genera. In addition, these isolates were tested for antimicrobial activity and the presence of polyketide synthase and non-ribosomal peptide synthetase genes. This study confirms the significant biodiversity of actinobacteria in the Norwegian marine habitats, and their potential for producing biologically active compounds.     

Actinomycetes biosynthetic potential: how to bridge in silico and in vivo?

Actinomycetes genome sequencing and bioinformatic analyses revealed a large number of “cryptic” gene clusters coding for secondary metabolism. These gene clusters have the potential to increase the chemical diversity of natural products. Indeed, reexamination of well-characterized actinomycetes strains revealed a variety of hidden treasures. Growing information about this metabolic diversity has promoted further development of strategies to discover novel biologically active compounds produced by actinomycetes. This new task for actinomycetes genetics requires the development and use of new approaches and tools. Application of synthetic biology approaches led to the development of a set of strategies and tools to satisfy these new requirements. In this review, we discuss strategies and methods to discover small molecules produced by these fascinating bacteria and also discuss a variety of genetic instruments and regulatory elements used to activate secondary metabolism cryptic genes for the overproduction of these metabolites.     

Engineering Escherichia coli for production of functionalized terpenoids using plant P450s

Terpenoids are a highly diverse class of natural products that have historically provided a rich source for discovery of pharmacologically active small molecules, such as paclitaxel (Taxol) and artemisinin. Unfortunately, these secondary metabolites are typically produced in low abundance in their host organism, and their isolation consequently suffers from low yields and high consumption of natural resources. Furthermore, chemical synthesis of terpenoids can also be difficult to scale for industrial production. For these reasons, an attractive alternative strategy is to engineer metabolic pathways for production of pharmaceuticals or their precursors in a microbial host such as Escherichia coli. A key step is developing methods to carry out cytochrome P450 (P450)-based oxidation chemistry in vivo. Toward this goal, we have assembled two heterologous pathways for the biosynthesis of plant-derived terpenoid natural products, and we present the first examples of in vivo production of functionalized terpenoids in E. coli at high titer using native plant P450s.     

The asymmetric hydroformylation in the synthesis of pharmaceuticals.

The asymmetric hydroformylation reaction represents a potential powerful synthetic tool for the preparation of large number of different chiral products to be used as precursors of several organic compounds endowed with therapeutic activity. Essential and nonessential amino acids, 2-arylpropanoic acids, aryloxypropyl- and beta-phenylpropylamines, modified beta-phenylethylamines, pheniramines, and other classes of pharmaceuticals are available through enantioselective oxo-reaction of appropriate functionalized olefins; this process is catalyzed by rhodium or platinum complexes with chiral ligands, mainly chelating phosphines, and sometimes affords very high enantiomeric excesses. Furthermore, the application of many simple optically active aldehydes arising from asymmetric hydroformylation as chiral building blocks for the synthesis of complex pharmacologically active molecules such as antibiotics, peptides, antitumor macrocycle compounds, and prostaglandins is conveniently emphasized. The possibility of a future application of this asymmetric process for the production of many synthons to obtain other valuable pharmaceuticals is widely discussed too.     

Synthesis of octahydropyrano[3,2-b]pyrrole-2-carboxylic acid derivatives from D-mannose

Bicyclic amino acids are useful building blocks in synthesizing biologically active molecules and peptidomimetics. 2-Carboxy-6-hydroxyloctahydroindole (Choi) is a novel bicyclic amino acid found in the marine natural products aeruginosins. Many compounds in the aeruginosin family exhibit inhibition activities toward serine proteases including thrombin and trypsin. The unique Choi structure is the common feature of this family of oligopeptides and this motif is important for their observed biological activities. To better understand the influence of the stereochemistry of the Choi core structure on the inhibition activities, we have previously synthesized ring-oxygenated variants from glucose. The preparation of octahydro-pyrano[3,2-b]pyrrole 2-carboxylic acids from d-mannose is reported here. These novel bicyclic amino acids can be used in the preparation of aeruginosin analogs, as well as conformationally constrained peptidomimetics or other biologically active molecules.