The regulation of the secondary metabolism of Streptomyces: new links and experimental advances

Streptomycetes and other actinobacteria are renowned as a rich source of natural products of clinical, agricultural and biotechnological value. They are being mined with renewed vigour, supported by genome sequencing efforts, which have revealed a coding capacity for secondary metabolites in vast excess of expectations that were based on the detection of antibiotic activities under standard laboratory conditions. Here we review what is known about the control of production of so-called secondary metabolites in streptomycetes, with an emphasis on examples where details of the underlying regulatory mechanisms are known. Intriguing links between nutritional regulators, primary and secondary metabolism and morphological development are discussed, and new data are included on the carbon control of development and antibiotic production, and on aspects of the regulation of the biosynthesis of microbial hormones. Given the tide of antibiotic resistance emerging in pathogens, this review is peppered with approaches that may expand the screening of streptomycetes for new antibiotics by awakening expression of cryptic antibiotic biosynthetic genes. New technologies are also described that have potential to greatly further our understanding of gene regulation in what is an area fertile for discovery and exploitation     

Modern Industrial Microbiological Fermentations and Their Effects on Technical Developments

Owing to the development of many new processes and techniques, the production of primary and secondary metabolites with the aid of microorganisms has not only expanded greatly, but has also been simplified in many details, and has therefore become more widely feasible on the industrial scale. The present article surveys the principal fermentation processes and the main types of equipment, which shows a trend toward continuous processes and increasing automation. Some recent developments observed e.g. in the cultivation of animal cells or the production of electrical energy, and particularly in the production of proteins by microorganisms, are also described.     

共生菌——新活性天然产物的重要来源

共生菌是长期与宿主共同生活的一大类群的特殊微生物,过去长期被忽略,相关研究相对薄弱。事实上,因长期与宿主共进化,其生理生化特点更加鲜明、次生代谢产物合成更具特色。本文首先简单介绍了近年共生菌次生代谢产物的结构特点与生物学功能,然后对植物内生菌、昆虫共生菌、海绵共附生菌等重要共生微生物做了重点阐述。从已有研究结果来看,共生菌确系新活性天然产物的重要来源。     

Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics

Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a ‘grind-and-find’ study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.

Antimicrobial resistance is a major public concern and novel antibiotics are largely based on natural products. We summarize recent analytical and genome based technological developments that gain increasing importance in the natural products field.     

Some aspects of antibiotics research.

The era of spectacular developments in the field of antibiotics appears to be over. Ever greater efforts are needed to find ever fewer new antibiotics. The view that well-considered hypotheses can lead as successfully as proven results to further research is supported by the establishment of five theses. “Non-classical” screening methods and the search for secondary metabolites with unusual properties can provide a rich harvest.     

The upsurge of photocatalysts in antibiotic micropollutants treatment: Materials design,recovery, toxicity and bioanalysis

The excessive use of antimicrobial agents such as antibiotics and disinfectants for domestic purposes and industries polluted the water bodies severely in the recent past. Thus released antimicrobial agents negatively impact the environment and human health as it induce antimicrobial resistance (AMR) to microbes in the environment. Conventional biodegradation routes showed feasible antibiotics pollutants degradation. Nonetheless, they often demand a long time of operation (usually in days) and a major portion of the antimicrobial agents is left untreated unlike the complete oxidation with advanced oxidation processes. The residues of antibiotics left in the water bodies accelerate growth of microorganisms (bacterial, fungal, and viral) with AMR. In virtue of avoiding the catastrophe of widespread AMR, photocatalysis assisted antibiotic pollutant treatment is recently gaining a great popularity as an advanced oxidation process and has shown to be useful for the removal of antimicrobial compounds, mainly antibiotics. Recent review reports on photocatalytic antibiotic degradation focus on summarizing materials progress and antibiotics pollutants in chronological viewpoints. However, the relationship between photocatalytic materials and antibiotics oxidation reaction pathways and the toxicity of by-products are needed to be shown with better clarity to transfer the photocatalysis technique from lab to market in a safe way. This review critically analyzes the insights of energetic semiconductor structure lacking to achieve hydroxyl and superoxide radicals mediated antibiotics degradation, recommends new materials design (Z scheme) and standardization in the experimental designs, and also informs the influencing parameters on antibiotic degradation. It further assesses the possibility of recovering value-added chemicals from the photocatalytic treatment process and highlights the importance of environmental toxicity analysis. Overall, this review will be a resourceful guide for interdisciplinary researchers working on advanced photocatalysis and pharmaceutical pollutant treatment for achieving a sustainable ecology and initiating a circular economy in chemical industries.     

A Glossary for Chemical Approaches towards Unlocking the Trove of Metabolic Treasures in Actinomycetes

Actinobacterial natural products showed a critical basis for the discovery of new antibiotics as well as other lead secondary metabolites. Varied environmental and physiological signals touch the antibiotic machinery that faced a serious decline in the last decades. The reason was exposed by genomic sequencing data, which revealed that Actinomycetes harbor a large portion of silent biosynthetic gene clusters in their genomes that encrypt for secondary metabolites. These gene clusters are linked with a great reservoir of yet unknown molecules, and arranging them is considered a major challenge for biotechnology approaches. In the present paper, we discuss the recent strategies that have been taken to augment the yield of secondary metabolites via awakening these cryptic genes in Actinomycetes with emphasis on chemical signaling molecules used to induce the antibiotics biosynthesis. The rationale, types, applications and mechanisms are discussed in detail, to reveal the productive path for the unearthing of new metabolites, covering the literature until the end of 2020.     

Plants as sources of new antimicrobials and resistance-modifying agents

Covering: up to November 2011Infections caused by multidrug-resistant bacteria are an increasing problem due to the emergence and propagation of microbial drug resistance and the lack of development of new antimicrobials. Traditional methods of antibiotic discovery have failed to keep pace with the evolution of resistance. Therefore, new strategies to control bacterial infections are highly desirable. Plant secondary metabolites (phytochemicals) have already demonstrated their potential as antibacterials when used alone and as synergists or potentiators of other antibacterial agents. The use of phytochemical products and plant extracts as resistance-modifying agents (RMAs) represents an increasingly active research topic. Phytochemicals frequently act through different mechanisms than conventional antibiotics and could, therefore be of use in the treatment of resistant bacteria. The therapeutic utility of these products, however, remains to be clinically proven. The aim of this article is to review the advances in in vitro and in vivo studies on the potential chemotherapeutic value of phytochemical products and plant extracts as RMAs to restore the efficacy of antibiotics against resistant pathogenic bacteria. The mode of action of RMAs on the potentiation of antibiotics is also described.     

Carbohydrate-Based Antibiotics: A New Approach to Tackling the Problem of Resistance

Recent interest in the problem of antibiotic resistance has led to the identification of new targets and strategies for antibiotic discovery. Among these efforts, the development of small molecules as antibiotics to target carbohydrate receptors or carbohydrate-modifying enzymes represents a new direction. This review covers recent work in this regard and discusses the impact of each strategy on the development of drug resistance. Particularly interesting targets include unique cell-surface carbohydrates, the transglycosylase involved in peptidoglycan biosynthesis, and bacterial RNA. With a greater understanding of the genome of different bacteria as well as advances in functional genomics and proteomics, we can expect the discovery of a variety of targets for the development of novel antibiotics.     

UPLC-MS-Based Metabolomic Study of Streptomyces Strain HCCB10043 Under Different pH Conditions Reveals Important Pathways Affecting the Biosynthesis of A21978C Compounds

The A21978C family of compounds includes precursors of daptomycin, an important antibiotic for the treatment of diseases infected by Gram-positive resistant bacteria. Focusing on these valuable compounds, the differences in metabolites obtained with or without pH control in their producing strain Streptomyces parvus HCCB10043 were investigated by comparative metabolomics analysis based on UPLC-TOF-MS technology. According to principal component analysis, there were fourteen biomarker compounds selected under the two pH culture conditions. The ten known compounds were divided into two types: a glycoside family participating in the primary metabolism (daidzein, glycitein, genistein, and soyasaponin Bb) and a peptide family of secondary metabolites (valistatin, bestatin, 3-amino-2-hydroxy-4-phenylbutanoylvalylisoleucine, and arylomycins A2, A4, and A5). Through orthogonal partial least squares-discriminant analysis, three compounds, soyasaponin Bb and arylomycins A2 and A4 were identified as the most relevant compounds to A21978C1-3 production, the glycolytic pathway, and the NRPS synthesis pathway. The competitive relationship between arylomycin and A21978C was verified. These results have demonstrated the usefulness of the metabolomic strategy based on UPLC-MS in studying significant metabolic changes in actinomycetes. Moreover, this metabolomic strategy can provide new ideas and guidance for the regulation and improvement of secondary metabolites production.     

Additive effect of Lygodium venustum SW. in association with gentamicin

The aim of this work was to evaluate the interactions between gentamicin and the ethanol extract of the fern Lygodium venustum SW (EELV). The ethanol extract of L. venustum was obtained, the phytocompounds were identified and the EELV was assayed by the checkerboard method with gentamicin against two bacterial strains multiresistant to antibiotics. The antibiotic activity of gentamicin, when associated with the extract, was enhanced in an additive manner against both strains. The results indicated that L. venustum can be a source of secondary metabolites to be used in association with antibiotics as aminoglycosides in the antibiotic chemotherapy against resistant bacteria.     

Small molecule inhibition of microbial natural product biosynthesis-an emerging antibiotic strategy

A variety of natural products modulate critical biological processes in the microorganisms that produce them. Thus, inhibition of the corresponding natural product biosynthesis pathways represents a promising avenue to develop novel antibiotics. In this tutorial review, we describe several recent examples of designed small molecule inhibitors of microbial natural product biosynthesis and their use in evaluating this emerging antibiotic strategy.     

Novel Chemical and Biological Insights of Inositol Derivatives in Mediterranean Plants

Inositols (Ins) are natural compounds largely widespread in plants and animals. Bio-sinthetically they derive from sugars, possessing a molecular structure very similar to the simple sugars, and this aspect concurs to define them as primary metabolites, even though it is much more correct to place them at the boundary between primary and secondary metabolites. This dichotomy is well represented by the fact that as primary metabolites they are essential cellular components in the form of phospholipid derivatives, while as secondary metabolites they are involved in a plethora of signaling pathways playing an important role in the surviving of living organisms. myo-Inositol is the most important and widespread compound of this family, it derives directly from d-glucose, and all known inositols, including stereoisomers and derivatives, are the results of metabolic processes on this unique molecule. In this review, we report the new insights of these compounds and their derivatives concerning their occurrence in Nature with a particular emphasis on the plant of the Mediterranean area, as well as the new developments about their biological effectiveness.     

Chip-calorimetric evaluation of the efficacy of antibiotics and bacteriophages against bacteria on a minute-timescale

Rapid detection of antibiotic resistances of clinical bacterial strains would allow an early selective antibiotic therapy and a faster intervention and implementation of infection control measurements. In clinical practice, however, conventional antibiotic susceptibility tests of bacteria often need 24 h until the results are obtained. The metabolic heat production of bacteria is an excellent possibility to record their physiological activities and could therefore be used for a rapid discrimination of bacterial strains which are resistant or non-resistant to antibiotics and also to lytic bacteriophages, respectively. Unfortunately, conventional calorimeters suffer from need of comparably large volumes of bacterial suspensions are characterised by slow operation and high costs which restrict their application in clinical laboratories. The present paper demonstrates that a new type of calorimeters developed on silicon-chip technology enables the detection of antibiotic resistances on a minute-timescale. For this reasons, a prototype chip calorimeter was used which sensitivity is 20 nW related to the heat production of about 10⁴ bacteria. For a clear discrimination of antibiotic resistance about 10⁵ bacteria are required. The antibiotic resistances and susceptibilities of different strains of Staphylococcus aureus to cefoxitin and the sensitivities of S. aureus DSM 18421 and E. coli DSM 498 to a mixture of two bacteriophages were studied. Comparing the heat productions of cultures incubated with antibiotics or bacteriophages to those without these antibacterial preparations enabled a clear discrimination of resistant and non-resistant strains already after totally 2 h.     

Plant cell culture technologies: A promising alternatives to produce high-value secondary metabolites

Plants have been used for its medicinal values since ancient time. The medicinal properties of plants are based on their phytochemical constituent particularly secondary metabolites which are produced in low amounts by plants. Secondary metabolites have been used as medicines, flavors, colors, and fragrances. In recent time, these natural compounds are gaining enormous attention in pharmaceutical, cosmetics, and nutraceutical industries and are regarded economically valuable products. The production of plant secondary metabolites in plant is largely dependent on the plant species, environmental factors and geographical regions. In addition, the main challenges in their mass production is reported to be the quality and quantity issues during their synthesis. Therefore, enthusiasm has grown for increasing the production of secondary metabolites by employing in vitro plant cell culture technology and bioengineering methods. Such technological advancement, has led to production of a huge number of medicinal herbs and high-value secondary metabolites that are mostly used in pharmaceuticals, cosmetics and nutraceuticals industries. The current mini-review article focuses on applications of plant cell culture system for the production secondary metabolites and recent techniques used to improve metabolite contents. Furthermore, our review emphasizes safety issues of plant cell culture derived products.     

Can Eucalyptol Replace Antibiotics?

One of the primary reasons for the search for new antimicrobial agents is the increasing and spreading resistance of microorganisms to previously used drugs. This is particularly important in the case of rapidly progressing infections that require the rapid administration of an appropriately selected antibiotic. However, along with the administration of antibiotics, complications in the disease-weakened body may arise in the form of systemic mycoses, viral infections, and protozoan infections. Therefore, there is an increasing interest among researchers focusing on the use of naturally occurring terpenic compounds in stand-alone or combined therapies with antibiotics. In this publication, the aim of our work is to present the results of a literature review on the antimicrobial activity of eucalyptol.     

Valorization of Winemaking By-Products as a Novel Source of Antibacterial Properties: New Strategies to Fight Antibiotic Resistance

The emergence of antibiotic-resistance in bacteria has limited the ability to treat bacterial infections, besides increasing their morbidity and mortality at the global scale. The need for alternative solutions to deal with this problem is urgent and has brought about a renewed interest in natural products as sources of potential antimicrobials. The wine industry is responsible for the production of vast amounts of waste and by-products, with associated environmental problems. These residues are rich in bioactive secondary metabolites, especially phenolic compounds. Some phenolics are bacteriostatic/bactericidal against several pathogenic bacteria and may have a synergistic action towards antibiotics, mitigating or reverting bacterial resistance to these drugs. Complex phenolic mixtures, such as those present in winemaking residues (pomace, skins, stalks, leaves, and especially seeds), are even more effective as antimicrobials and could be used in combined therapy, thereby contributing to management of the antibiotic resistance crisis. This review focuses on the potentialities of winemaking by-products, their extracts, and constituents as chemotherapeutic antibacterial agents.     

Recent advances in electrochemical sensors for antibiotics and their applications

The abuse of antibiotics will cause an increase of drug-resistant strains and environmental pollution,which in turn will affect human health.Therefore,it is important to develop effective detection techniques to determine the level of antibiotics contamination in various fields.Compared with traditional detection methods,electrochemical sensors have received extensive attention due to their advantages such as high sensitivity,low detection limit,and good selectivity.In this mini review,we summarized the latest developments and new trends in electrochemical sensors for antibiotics.Here,modification methods and materials of electrode are discussed.We also pay more attention to the practical applications of antibiotics electrochemical sensors in different fields.In addition,the existing problems and the future challenges ahead have been proposed.We hope that this review can provide new ideas for the development of electrochemical sensors for antibiotics in the future.     

Chemical ecology of endophytic fungi: origins of secondary metabolites

Endophytes constitute a remarkably multifarious group of microorganisms ubiquitous in plants and maintain an imperceptible association with their hosts for at least a part of their life cycle. Their enormous biological diversity coupled with their capability to biosynthesize bioactive secondary metabolites has provided the impetus for a number of investigations on endophytes. Here, we highlight the possible current and future strategies of understanding the chemical communication of endophytic fungi with other endophytes (fungi and bacteria) and with their host plants, which might not only allow the discovery and sustainable production of desirable natural products but also other mostly overlooked bioactive secondary metabolites.     

Spatial regulation of a common precursor from two distinct genes generates metabolite diversity

In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPS-like genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. In hyphae this compound is converted to aspulvinones whereas in conidia it is converted to melanin. The genes are expressed in different tissues and this spatial control is probably regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is located in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. Our data reveal the first case in secondary metabolite biosynthesis in which the tissue specific production of a single compound directs it into two separate pathways, producing distinct compounds with different functions. Our data also reveal that a single trans-prenyltransferase, AbpB, prenylates two substrates, aspulvinones and butyrolactones, revealing that genes outside of contiguous secondary metabolism gene clusters can modify more than one compound thereby expanding metabolite diversity. Our study raises the possibility of incorporation of spatial, cell-type specificity in expression of secondary metabolites of biological interest and provides new insight into designing and reconstituting their biosynthetic pathways.