Some aspects of overproduction of secondary metabolites

Different approaches used to increase production of secondary metabolites and construct overproducing strains of microorganisms are reviewed. Overproduction of secondary metabolites incuudes the physiological control,e.g. feed-back inhibition, carbon and energy source regulation, nitrogen source regulation, phosphate regulation and the effect of autoregulatory compounds. The genetic control of overproduction of secondary metabolites includes mechanisms similar to those controlling the expression of primary metabolism coding genes, although the genes specifying biosynthesis of secondary metabolites and their expression have some particular features. Possible future trends in the study of overproduction of secondary metabolites are discussed. Dedicated to the 70th birthday of Dr. Z. Vanêk     

Biotechnologische Produktion mikrobieller Wirkstoffe: ein Beispiel für die Nutzung des Adaptationspotentials von Mikroorganismen

The role of the microbial secondary metabolism in the cytodifferentiation of producer strains and in the ecological system is reviewed. The production of bioactive metabolites such as antibiotics seems to play a role in long-term strategies of adaptation to environmental changes. This is reflected by characteristic features of regulation of the secondary metabolism such as catabolite repression, lack of uniform regulatory mechanisms and limited specificity of enzymes involved. The examples given may show that advantages have been taken from the knowledge of special regulatory features with regard to strain improvement and the designing of the metabolite spectrum.     

Functional analysis of colonic bacterial metabolism: relevant to health?

With the use of molecular techniques, numerous studies have evaluated the composition of the intestinal microbiota in health and disease. However, it is of major interest to supplement this with a functional analysis of the microbiota. In this review, the different approaches that have been used to characterize microbial metabolites, yielding information on the functional end products of microbial metabolism, have been summarized. To analyze colonic microbial metabolites, the most conventional way is by application of a hypothesis-driven targeted approach, through quantification of selected metabolites from carbohydrate (e.g., short-chain fatty acids) and protein fermentation (e.g., p-cresol, phenol, ammonia, or H(2)S), secondary bile acids, or colonic enzymes. The application of stable isotope-labeled substrates can provide an elegant solution to study these metabolic pathways in vivo. On the other hand, a top-down approach can be followed by applying metabolite fingerprinting techniques based on (1)H-NMR or mass spectrometric analysis. Quantification of known metabolites and characterization of metabolite patterns in urine, breath, plasma, and fecal samples can reveal new pathways and give insight into physiological regulatory processes of the colonic microbiota. In addition, specific metabolic profiles can function as a diagnostic tool for the identification of several gastrointestinal diseases, such as ulcerative colitis and Crohn's disease. Nevertheless, future research will have to evaluate the relevance of associations between metabolites and different disease states.     

Proteomics and metabolomics: the molecular make-up of toxic aromatic pollutant bioremediation

Microbial-mediated attenuation of toxic aromatic pollutants offers great potential for the restoration of contaminated environments in an ecologically acceptable manner. However, incomplete biological information regarding the regulation of growth and metabolism in many microbial communities restricts progress in the site-specific mineralization process. In the postgenomic era, recent advances in MS have allowed enormous progress in proteomics and elucidated many complex biological interactions. These research forefronts are now expanding toward the analysis of low-molecular-weight primary and secondary metabolites analysis, i.e., metabolomics. The advent of 2-DE in conjunction with MS offers a promising approach to address the molecular mechanisms of bioremediation. The two fields of proteomics and metabolomics have thus far worked separately to identify proteins and primary and secondary metabolites during bioremediation. A simultaneous study combining functional proteomics and metabolomics, i.e., proteometabolomics would create a system-wide approach to studying site-specific microorganisms during active mineralization processes. This article deals with advances in environmental proteomics and metabolomics and advocates the simultaneous study of both technologies to implement cell-free bioremediation.     

Metabolic regulation of fermentation processes

To compete in nature against other forms of life, microorganisms possess regulatory mechanisms which control production of their metabolites, thus, protecting against overproduction and excretion of these primary and secondary metabolites into the environment. To effect such an economical form of life, they possess regulatory mechanisms which control production of these metabolites and protect against overproduction and excretion into the environment of excess concentrations. In the field of industrial fermentation, the opposite concept prevails. Fermentation microbiologists search for a rare overproducing strain in nature, then further deregulate the microorganism so that it overproduces huge quantities of a desired commercially important product such as a metabolite or an enzyme. Deregulation is brought about by nutritional as well as classical and molecular genetic manipulations to bypass and/or remove negative regulatory mechanisms and to enhance positive regulatory mechanisms. These mechanisms include induction, nutritional regulation by sources of carbon, nitrogen and phosphorus, and feedback control. The controls and their modification by biotechnologists are the subjects of this review.     

Application of cell technologies for production of plant-derived bioactive substances of plant origin

Bioactive substances (BAS) of plant origin are known to play a very important role in modern medicine. Their use, however, is often limited by availability of plant resources and may jeopardize rare species of medicinal plants. Plant cell cultures can serve as a renewable source of valuable secondary metabolites. To the date, however, only few examples of their commercial use are known. The main reasons for such a situation are the insufficient production of secondary metabolites and high cultivation costs. It is possible to increase the performance of plant cell cultures by one or two orders of magnitude using traditional methods, such as selection of highly productive strains, optimization of the medium composition, elicitation, and addition of precursors of secondary metabolite biosynthesis. The progress in molecular biology methods brought about the advent of new means for increasing of the productivity of cell cultures based on the methods of metabolic engineering. Thus, overexpression of genes encoding the enzymes involved in the synthesis of the target product or, by contrast, repression of these genes significantly influences the cell biosynthetic capacity in vitro. Nevertheless, the attempts of the production of many secondary metabolites in plant cell culture were unsuccessful so far, probably due to the peculiarities of the cell culture as an artificial population of plant somatic cells. The use of plant organ culture or transformed roots (hairy root) could turn to be a considerably more efficient solution for this problem. The production of plant-derived secondary metabolites in yeast or bacteria transformed with plant genes is being studied currently. Although the attempts to use metabolic engineering methods were not particularly successful so far, new insights in biochemistry and physiology of secondary metabolism, particularly in regulation and compartmentation of secondary metabolite synthesis as well as mechanisms of their transport and storage make these approaches promising.     

Evolutionary basis and ecological role of toxic microbial secondary metabolites

This presentation develops a theory of the evolutionary origin and ecological implications of toxic microbial secondary metabolites. The theory is based on a model system that outlines cause—effect associations between pertinent biotypes in the aflatoxin contamination of developing maize kernels. The model suggests that the aflatoxin-producing fungi are natural digestive tract inhabitants of a number of insect species that feed on developing kernels. During feeding, the insect larvae introduce fungal propagules and provide infection sites on damaged kernels. The fungal association with insects exhibits extraordinary variability, ranging from symbiotic to pathogenic. Elaboration of aflatoxin by the fungus facilitates the pathogenic process in host insects. The theory contends that genetic information for secondary microbial metabolites evolved during ecosystem disequilibria. During periods of ecological stability, mechanisms evolved for repression of toxic secondary metabolite biosynthesis. The theory broadly suggests that contemporary agricultural activities presents the requisite milieu for production or toxic microbial secondary metabolites.     

Peptide siderophores

Siderophores are low molecular weight iron chelators, produced by virtually all bacteria, fungi and some plants. They serve to deliver the essential element iron, barely soluble under aerobic conditions, into microbial cells. Siderophores are therefore important secondary metabolites which are very often based on amino acids and their derivatives. Biosynthesis, transport, regulation and chemical synthesis of natural siderophores and their analogues is of considerable interest for the protein and peptide chemist. This review gives an overview of the structural classes of peptidic siderophores, along with data on their biosynthesis. On a number of representative examples, strategies and schemes of their chemical synthesis are described. ©1998 European Peptide Society and John Wiley & Sons, Ltd.     

昆虫对植物次生物质的代谢适应机制及其对昆虫抗药性的意义

植物次生物质(plant secondary metabolites)对昆虫的取食行为、生长发育及繁殖可以产生不利影响,甚至对昆虫可以产生毒杀作用。为了应对植物次生物质的不利影响,昆虫通过对植物次生物质忌避取食、解毒代谢等多种机制,而对寄主植物产生适应性。其中,昆虫的解毒代谢酶包括昆虫细胞色素P450酶系（P450s）及谷胱甘肽硫转移酶（GSTs）等,在昆虫对植物次生物质的解毒代谢及对寄主植物的适应性中发挥了重要作用。昆虫的解毒酶系统不仅可以代谢植物次生物质,还可能代谢化学杀虫剂,因而昆虫对寄主植物的适应性与其对杀虫剂的耐药性甚至抗药性密切相关。昆虫细胞色素P450s和GSTs等代谢解毒酶活性及相关基因的表达可以被植物次生物质影响,这不仅使昆虫对寄主植物的防御产生了适应性,还影响了昆虫对杀虫剂的解毒代谢,因而改变昆虫的耐药性或抗药性。掌握昆虫对植物次生物质的代谢适应机制及其在昆虫抗药性中的作用,对于明确昆虫的抗药性机制具有重要的参考意义。本文综述了植物次生物质对昆虫的影响、昆虫对寄主植物次生物质的代谢机制、昆虫对植物次生物质的代谢适应性对昆虫耐药性及抗药性的影响等方面的研究进展。     

Biosynthesis of plant-specific stilbene polyketides in metabolically engineered Escherichia coli

Background  

Phenylpropanoids are the precursors to a range of important plant metabolites such as the cell wall constituent lignin and the secondary metabolites belonging to the flavonoid/stilbene class of compounds. The latter class of plant natural products has been shown to function in a wide range of biological activities. During the last few years an increasing number of health benefits have been associated with these compounds. In particular, they demonstrate potent antioxidant activity and the ability to selectively inhibit certain tyrosine kinases. Biosynthesis of many medicinally important plant secondary metabolites, including stilbenes, is frequently not very well understood and under tight spatial and temporal control, limiting their availability from plant sources. As an alternative, we sought to develop an approach for the biosynthesis of diverse stilbenes by engineered recombinant microbial cells.     

Involvement of nitrogen-containing compounds in beta-lactam biosynthesis and its control

Biosynthesis of beta-lactam antibiotics by fungi and actinomycetes is markedly affected by compounds containing nitrogen. The different processes employed by the spectrum of microbes capable of making these valuable compounds are affected differently by particular compounds. Ammonium ions, except at very low concentrations, exert negative effects via nitrogen metabolite repression, sometimes involving the nitrogen regulatory gene nre. Certain amino acids are precursors or inducers, whereas others are involved in repression and, in certain cases, as inhibitors of biosynthetic enzymes and of enzymes supplying precursors. The most important amino acids from the viewpoint of regulation are lysine, methionine, glutamate and valine. Surprisingly, diamines such as diaminopropane, putrescine and cadaverine induce cephamycin production by actinomycetes. In addition to penicillins and cephalosporins made by fungi and cephamycins made by actinomycetes, other beta-lactams are made by actinomycetes and unicellular bacteria. These include clavams (e.g., clavulanic acid), carbapenems (e.g., thienamycin), nocardicins and monobactams. Here also, amino acids are precursors and inhibitors, but only little is known about regulation. In the case of the simplest carbapenem made by unicellular bacteria, i.e., 1-carba-2-em-3-carboxylic acid, quorum sensors containing homoserine lactone are inducers.     

Metabolomics methods for the synthetic biology of secondary metabolism

Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or "awakening" of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent advances in DNA sequencing and synthesis to achieve unprecedented control over metabolic pathways. One of the indispensable tools in the synthetic biology toolbox is metabolomics, the global quantification of small biomolecules. This review illustrates the pivotal role of metabolomics for the synthetic microbiology of secondary metabolism, including its crucial role in novel compound discovery in microbes, the examination of side products of engineered metabolic pathways, as well as the identification of major bottlenecks for the overproduction of compounds of interest, especially in combination with metabolic modeling. We conclude by highlighting remaining challenges and recent technological advances that will drive metabolomics towards fulfilling its potential as a cornerstone technology of synthetic microbiology.     

Metabolic engineering: techniques for analysis of targets for genetic manipulations

Metabolic engineering has been defined as the purposeful modification of intermediary metabolism using recombinant DNA techniques. With this definition metabolic engineering includes: (1) inserting new pathways in microorganisms with the aim of producing novel metabolites, e.g., production of polyketides by Streptomyces; (2) production of heterologous peptides, e.g., production of human insulin, erythropoitin, and tPA; and (3) improvement of both new and existing processes, e.g., production of antibiotics and industrial enzymes. Metabolic engineering is a multidisciplinary approach, which involves input from chemical engineers, molecular biologists, biochemists, physiologists, and analytical chemists. Obviously, molecular biology is central in the production of novel products, as well as in the improvement of existing processes. However, in the latter case, input from other disciplines is pivotal in order to target the genetic modifications; with the rapid developments in molecular biology, progress in the field is likely to be limited by procedures to identify the optimal genetic changes. Identification of the optimal genetic changes often requires a meticulous mapping of the cellular metabolism at different operating conditions, and the application of metabolic engineering to process optimization is, therefore, expected mainly to have an impact on the improvement of processes where yield, productivity, and titer are important design factors, i.e., in the production of metabolites and industrial enzymes. Despite the prospect of obtaining major improvement through metabolic engineering, this approach is, however, not expected to completely replace the classical approach to strain improvement-random mutagenesis followed by screening. Identification of the optimal genetic changes for improvement of a given process requires analysis of the underlying mechanisms, at best, at the molecular level. To reveal these mechanisms a number of different techniques may be applied: (1) detailed physiological studies, (2) metabolic flux analysis (MFA), (3) metabolic control analysis (MCA), (4) thermodynamic analysis of pathways, and (5) kinetic modeling. In this article, these different techniques are discussed and their applications to the analysis of different processes are illustrated.     

Metabolomics assisted metabolic network modeling and network wide analysis of metabolites in microbiology

Metabolomics is the science of qualitatively and quantitatively analyzing low molecular weight metabolites occur in a given biological system. It provides valuable information to elucidate the functional roles and relations of different metabolites in a metabolic pathway. In recent years, a large amount of research on microbial metabolomics has been conducted. It has become a useful tool for achieving highly efficient synthesis of target metabolites. At the same time, many studies have been conducted over the years in order to integrate metabolomics data into metabolic network modeling, which has yielded many exciting results. Additionally, metabolomics also shows great advantages in analyzing the relationship of metabolites network wide. Integrating metabolomics data into metabolic network construction and applying it in network wide analysis of cell metabolism would further improve our ability to control cellular metabolism and optimize the design of cell factories for the overproduction of valuable biochemicals. This review will examine recent progress in the application of metabolomics approaches in metabolic network modeling and network wide analysis of microbial cell metabolism.     

Cholesterol, an essential molecule: diverse roles involving cytochrome P450 enzymes

Cholesterol is an essential molecule for eukaryotic life and is an important precursor for a wide range of physiological processes. Biosynthesis and homoeostasis of cholesterol are complex mechanisms that are tightly regulated and interlinked with activities of a number of cytochrome P450 enzymes. These P450s play central critical roles in cholesterol metabolism. Key roles include a rate-limiting reaction in the synthesis of cholesterol itself, and in the oxidative transformations of cholesterol into steroid hormones and bile acids. However, microbial P450s also have important roles that impinge directly on human cholesterol synthesis and oxidation. Recent data reveal that Mycobacterium tuberculosis (which infects more than one-third of the world's human population) uses P450s to initiate breakdown of host cholesterol as an energy source. Microbial P450s also catalyse industrially important transformations in the synthesis of cholesterol-lowering statin drugs, with clear benefits to humans. The present article reviews the various roles of P450s in human cholesterol metabolism, from endogenous P450s through to microbial oxidases that enable catabolism of human cholesterol, or facilitate production of statins that regulate cholesterol production with positive outcomes in cardiovascular disease.     

Starch-based plastic polymer degradation by the white rot fungus Phanerochaete chrysosporium grown on sugarcane bagasse pith: enzyme production

In this study, starch metabolites and enzymes were determined during starch-based plastic polymer biodegradation by the white rot fungus Phanerochaete chrysosporium, grown in sugarcane bagasse pith in tubular reactors. Various metabolites, amylase, ligninase and cellulase production were measured during P. chrysosporium growth on sugarcane bagasse pith with added glucose and starch polymer. On-line respirometric analyses followed during 32 days confirmed the P. chrysosporium capability of growing on sugarcane bagasse pith with starch polymer degradation. Enzyme activity during secondary metabolism increased, and a 70% and 74% starch degradation was reached with and without glucose addition, generating low molecular weight metabolites (e.g.) dextrin, maltotriose, maltose and glucose that were detected by high performance liquid chromatography.     

Evolutionary recruitment of a flavin-dependent monooxygenase for stabilization of sequestered pyrrolizidine alkaloids in arctiids

Pyrrolizidine alkaloids are secondary metabolites that are produced by certain plants as a chemical defense against herbivores. They represent a promising system to study the evolution of pathways in plant secondary metabolism. Recently, a specific gene of this pathway has been shown to have originated by duplication of a gene involved in primary metabolism followed by diversification and optimization for its specific function in the defense machinery of these plants. Furthermore, pyrrolizidine alkaloids are one of the best-studied examples of a plant defense system that has been recruited by several insect lineages for their own chemical defense. In each case, this recruitment requires sophisticated mechanisms of adaptations, e.g., efficient excretion, transport, suppression of toxification, or detoxification. In this review, we briefly summarize detoxification mechanism known for pyrrolizidine alkaloids and focus on pyrrolizidine alkaloid N-oxidation as one of the mechanisms allowing insects to accumulate the sequestered toxins in an inactivated protoxic form. Recent research into the evolution of pyrrolizidine alkaloid N-oxygenases of adapted arctiid moths (Lepidoptera) has shown that this enzyme originated by the duplication of a gene encoding a flavin-dependent monooxygenase of unknown function early in the arctiid lineage. The available data suggest several similarities in the molecular evolution of this adaptation strategy of insects to the mechanisms described previously for the evolution of the respective pathway in plants.     

Strain improvement for fermentation and biocatalysis processes by genetic engineering technology

Twenty years ago, the first complete gene cluster encoding the actinorhodin biosynthetic pathway was cloned and characterized. Subsequently, the gene clusters encoding the biosynthetic pathways for many antibiotics were isolated. In the past decade, breakthroughs in technology brought that generation of rationally designed or new hybrid metabolites to fruition. Now, the development of high-throughput DNA sequencing and DNA microarray techniques enables researchers to identify the regulatory mechanisms for the overproduction of secondary metabolites and to monitor gene expression during the fermentation cycle, accelerating the rational application of metabolic pathway engineering. How are the new tools of biotechnology currently being applied to improve the production of secondary metabolites? Where will this progress lead us tomorrow? The use of whole cells or partially purified enzymes as catalysts has been increased significantly for chemical synthesis in pharmaceutical and fine-chemical industries. The development of PCR technologies for protein engineering and DNA shuffling is leading to the generation of new enzymes with increased stability to a wide range of pHs, temperatures and solvents and with increased substrate specificity, reaction rate and enantioselectivity. Where will this emerging technology lead us in the twenty-first century?