Microbial genomics for the improvement of natural product discovery

Genome mining for new enediyne antibiotics

Enediyne antibiotics epitomize nature's chemical creativity. They contain intricate molecular architectures that are coupled with potent biological activities involving double-stranded DNA scission. The recent explosion in microbial genome sequences has revealed a large reservoir of novel enediynes. However, while hundreds of enediyne biosynthetic gene clusters (BGCs) can be detected, less than two dozen natural products have been characterized to date as many clusters remain silent or sparingly expressed under standard laboratory growth conditions. This review focuses on four distinct strategies, which have recently enabled discoveries of novel enediynes: phenotypic screening from rare sources, biosynthetic manipulation, genomic signature-based PCR screening, and DNA-cleavage assays coupled with activation of silent BGCs via high-throughput elicitor screening. With an abundance of enediyne BGCs and emerging approaches for accessing them, new enediyne natural products and further insights into their biogenesis are imminent.

Chemical Epigenetic Regulation Secondary Metabolites Derived from Aspergillus sydowii DL1045 with Inhibitory Activities for Protein Tyrosine Phosphatases

Protein tyrosine phosphatases (PTPs) are ubiquitous in living organisms and are promising drug targets for cancer, diabetes/obesity, and autoimmune disorders. In this study, a histone deacetylase inhibitor called suberoylanilide hydroxamic acid (SAHA) was added to a culture of marine fungi (Aspergillus sydowii DL1045) to identify potential drug candidates related to PTP inhibition. Then, the profile of the induced metabolites was characterized using an integrated metabolomics strategy. In total, 46% of the total SMs were regulated secondary metabolites (SMs), among which 20 newly biosynthesized metabolites (10% of the total SMs) were identified only in chemical epigenetic regulation (CER) broth. One was identified as a novel compound, and fourteen compounds were identified from Aspergillus sydowii first. SAHA derivatives were also biotransformed by A. sydowii DL1045, and five of these derivatives were identified. Based on the bioassay, some of the newly synthesized metabolites exhibited inhibitory effects on PTPs. The novel compound sydowimide A (A11) inhibited Src homology region 2 domain-containing phosphatase-1 (SHP1), T-cell protein tyrosine phosphatase (TCPTP) and leukocyte common antigen (CD45), with IC50 values of 1.5, 2.4 and 18.83 μM, respectively. Diorcinol (A3) displayed the strongest inhibitory effect on SHP1, with an IC50 value of 0.96 μM. The structure-activity relationship analysis and docking studies of A3 analogs indicated that the substitution of the carboxyl group reduced the activity of A3. Research has demonstrated that CER positively impacts changes in the secondary metabolic patterns of A. sydowii DL1045. The compounds produced through this approach will provide valuable insights for the creation and advancement of novel drug candidates related to PTP inhibition.

NMR-Metabolomic Profiling and Genome Mining Drive the Discovery of Cyclic Decapeptides from a Marine Streptomyces

The integration of NMR-metabolomic and genomic analyses can provide enhanced identification of structural properties as well as key biosynthetic information, thus achieving the targeted discovery of new natural products. For this purpose, NMR-based metabolomic profiling of the marine-derived Streptomyces sp. S063 (CGMCC 14582) was performed, by which N-methylated peptides possessing unusual negative 1H NMR chemical shift values were tracked. Meanwhile, genome mining of this strain revealed the presence of an unknown NRPS gene cluster (len) with piperazic-acid-encoding genes (lenE and lenF). Under the guidance of the combined information, two cyclic decapeptides, lenziamides D1 (1) and B1 (2), were isolated from Streptomyces sp. S063, which contains piperazic acids with negative 1H NMR values. The structures of 1 and 2 were determined by extensive spectroscopic analysis combined with Marfey's method and ECD calculations. Furthermore, we provided a detailed model of lenziamide (1 and 2) biosynthesis in Streptomyces sp. S063. In the cytotoxicity evaluation, 1 and 2 showed moderate growth inhibition against the human cancer cells HEL, H1975, H1299, and drug-resistant A549-taxol with IC50 values of 8-24 μM.

Metabolomic Strategy to Characterize the Profile of Secondary Metabolites in Aspergillus aculeatus DL1011 Regulated by Chemical Epigenetic Agents

Chemical epigenetic regulation (CER) is an effective method to activate the silent pathway of fungal secondary metabolite synthesis. However, conventional methods for CER study are laborious and time-consuming. In the meantime, the overall profile of the secondary metabolites in the fungi treated by the CER reagent is not well characterized. In this study, suberohydroxamic acid (SBHA), a histone deacetylase inhibitor, was added to a culture of Aspergillus aculeatus DL1011 and a new strategy based on LC-MS/MS analysis integrated with various metabolomic tools (MetaboAnalyst, MS-DIAL, SIRIUS and GNPS) was developed to characterize the profile of induced metabolites. As a result, 13.6%, 29.5% and 27.2% of metabolites were identified as newly biosynthesized, increasing and decreasing in abundance by CER, respectively. The structures of the 18 newly induced secondary metabolites were further identified by the new strategy to demonstrate that 72.2% of them (1 novel compound and 12 known compounds) were first discovered in A. aculeatus upon SBHA treatment. The accuracy of the new approach was confirmed by purification and NMR data analysis of major newly biosynthesized secondary metabolites. The bioassay showed that the newly biosynthesized compounds, roseopurpurin analogues, showed selective activities against DPPH scavenging, cytotoxicity and SHP1 inhibition. Our research demonstrated that CER was beneficial for changing the secondary metabolic profile of fungi and was an effective means of increasing the diversity of active metabolites. Our work also supplied a metabolomic strategy to characterize the profile changes and determine the newly induced compounds in the secondary metabolites of fungi treated with the chemical epigenetic regulator.

Newly Discovered Mechanisms of Antibiotic Self-Resistance with Multiple Enzymes Acting at Different Locations and Stages

Self-resistance determinants are essential for the biosynthesis of bioactive natural products and are closely related to drug resistance in clinical settings. The study of self-resistance mechanisms has long moved forward on the discovery of new resistance genes and the characterization of enzymatic reactions catalyzed by these proteins. However, as more examples of self-resistance have been reported, it has been revealed that the enzymatic reactions contribute to self-protection are not confined to the cellular location where the final toxic compounds are present. In this review, we summarize representative examples of self-resistance mechanisms for bioactive natural products functional at different cell locations to explore the models of resistance strategies involved. Moreover, we also highlight those resistance determinants that are widespread in nature and describe the applications of self-resistance genes in natural product mining to interrogate the landscape of self-resistance genes in drug resistance-related new drug discovery.

Momomycin, an Antiproliferative Cryptic Metabolite from the Oxytetracycline Producer Streptomyces rimosus

Natural products provide an important source of pharmaceuticals and chemical tools. Traditionally, assessment of unexplored microbial phyla has led to new natural products. However, with every new microbe, the number of orphan biosynthetic gene clusters (BGC) grows. As such, the more difficult proposition is finding new molecules from well-studied strains. Herein, we targeted Streptomyces rimosus, the widely-used oxytetracycline producer, for the discovery of new natural products. Using MALDI-MS-guided high-throughput elicitor screening (HiTES), we mapped the global secondary metabolome of S. rimosus and structurally characterized products of three cryptic BGCs, including momomycin, an unusual cyclic peptide natural product with backbone modifications and several non-canonical amino acids. We elucidated important aspects of its biosynthesis and evaluated its bioactivity. Our studies showcase HiTES as an effective approach for unearthing new chemical matter from "drained" strains.

Exploration of genomic and functional features of chitinolytic bacterium Streptomyces chilikensis RC1830, isolated from Chilika Lake, India

Streptomyces chilikensis RC1830 was previously isolated as a novel chitinolytic streptomycete from Chilika Lake, Odisha, India. The strain RC1830 is a representative member of the soil-dwelling, filamentous Streptomyces group that produces the majority of natural antibiotics and secondary metabolites. The objective of this work was to assess the chitin degradation ability and whole-genome sequence of Streptomyces chilikensis RC1830. TLC analysis of the fermentation product revealed that strain RC1830 can convert shrimp shell colloidal chitin to N-acetylated chitooligosaccharides (N-AcCOS). A genome-wide investigation of RC1830 was also carried out to investigate the genetic basis for chitin breakdown. The result showed that the RC1830 genome possesses a chromosome with 7,121,774 bp (73.2% GC). The genome consists of 6807 coding sequences, 69 tRNA, and 3 rRNA genes. Furthermore, carbohydrate-active enzyme (CAZyme) analysis revealed that RC1830 has 89 glycoside hydrolase family genes, which could modulate the enzymes involved in the degradation of chitin ultimately producing industrially important COS. The whole-genome information of RC1830 could emphasize the mechanism involved in the RC1830's chitin breakdown activity, endowing RC1830 with a promising alternative for COS production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03184-5.

Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities

Covering: 2010 to 2021Organisms in nature have evolved into proficient synthetic chemists, utilizing specialized enzymatic machinery to biosynthesize an inspiring diversity of secondary metabolites. Often serving to boost competitive advantage for their producers, these secondary metabolites have widespread human impacts as antibiotics, anti-inflammatories, and antifungal drugs. The natural products discovery field has begun a shift away from traditional activity-guided approaches and is beginning to take advantage of increasingly available metabolomics and genomics datasets to explore undiscovered chemical space. Major strides have been made and now enable -omics-informed prioritization of chemical structures for discovery, including the prospect of confidently linking metabolites to their biosynthetic pathways. Over the last decade, more integrated strategies now provide researchers with pipelines for simultaneous identification of expressed secondary metabolites and their biosynthetic machinery. However, continuous collaboration by the natural products community will be required to optimize strategies for effective evaluation of natural product biosynthetic gene clusters to accelerate discovery efforts. Here, we provide an evaluative guide to scientific literature as it relates to studying natural product biosynthesis using genomics, metabolomics, and their integrated datasets. Particular emphasis is placed on the unique insights that can be gained from large-scale integrated strategies, and we provide source organism-specific considerations to evaluate the gaps in our current knowledge.

Metagenomics Unveils Posidonia oceanica "Banquettes" as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes)

Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." In recent years, interest in the potential uses of these P. oceanica banquettes has increased, and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, we performed a metagenomic study to investigate the microbial community associated with P. oceanica banquettes. Our results showed that the microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria. Pseudoalteromonas was the dominant genus, followed by Alteromonas, Labrenzia, and Aquimarina. The metagenome reads were binned and assembled into 23 nearly complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota, and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges, and hydrothermal vents, indicated that banquettes have numbers of natural products and carbohydrate active enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found. These results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes. IMPORTANCE Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concern due to their impact on beach use. Furthermore, Posidonia dry material has been considered a source of traditional remedies in several areas of the Mediterranean, and a few studies have been carried out to explore pharmacological activities of Posidonia extracts. The work presented here provides the first characterization of the microbiome associated with Posidonia banquettes. We carried out a metagenomic analysis together with an in-depth comparison of the banquette metagenome with 60 published metagenomes from different environments. This comparative analysis has unveiled the potential that Posidonia banquettes have for the synthesis of natural products, both in abundance (only surpassed by marine biofilms) and novelty. These products include mainly nonribosomal peptides and carbohydrate active enzymes. Thus, the interest of our work lies in the interest of Posidonia "waste" material as a source of new bioactive compounds and CAZymes.

A Leap Forward Towards Unraveling Newer Anti-infective Agents from an Unconventional Source: a Draft Genome Sequence Illuminating the Future Promise of Marine Heterotrophic Bacillus sp. Against Drug-Resistant Pathogens

During the previous decade, genome-built researches on marine heterotrophic microorganisms displayed the chemical heterogeneity of natural product resources coupled with the efficacies of harnessing the genetic divergence in various strains. Herein, we describe the whole genome data of heterotrophic Bacillus amyloliquefaciens MB6 (MTCC 12,716), isolated from a marine macroalga Hypnea valentiae, a 4,107,511-bp circular chromosome comprising 186 contigs, with 4154 protein-coding DNA sequences and a coding ratio of 86%. Simultaneously, bioactivity-guided purification of the bacterial extract resulted in six polyketide classes of compounds with promising antibacterial activity. Draft genome sequence of B. amyloliquefaciens MB6 unveiled biosynthetic gene clusters (BGCs) engaged in the biosynthesis of polyketide-originated macrolactones with prospective antagonistic activity (MIC ≤ 5 µg/mL) against nosocomial pathogens. Genome analysis manifested 34 putative BGCs necessitated to synthesize biologically active polyketide-originated frameworks or their derivatives. These results provide insights into the genetic basis of heterotrophic B. amyloliquefaciens MTCC 12,716 as a prospective lead for biotechnological and pharmaceutical applications.

Polyphenols Extraction From Vegetable Wastes Using a Green and Sustainable Method

Food systems have the potential to support human health, respecting the environmental sustainability principles. Food sustainability, enclosed in the concept of environmental sustainability, involves different aspects, including the recycling of food waste derived from the agri-food production chain, the use of biotechnologies ensuring the sustainability of the recovery processes of bioactive compounds from food waste and, last but not least, the awareness of having to consume and waste less food. Food loss and waste is generated during the whole supply chain, from production to household utilization. The utilization of agricultural wastes as an abundant, renewable and low-cost source for the production of high value-added products is currently explored. The bioactive compounds present in these sources have been proved to possess a wide range of biological activities; therefore, research is needed into the application of environmentally friendly traditional and advanced techniques with low production costs in the extraction, isolation and purification of phytochemical compounds from agricultural wastes in high yields and at maximal quality. Authors of this manuscript propose and discuss an innovative and sustainable extraction system of polyphenols from vegetable waste, based on an enzymatic pre-treatment coupled with a solid-liquid extraction by using a particular extractor (Naviglio Estrattore®). This extraction system, organic solvent free, allowed to extract relevant amount of polyphenols (flavonoids in particular) from several vegetable waste products.

New approaches for antituberculosis leads from Actinobacteria

Bioactive metabolites derived from the phylum Actinobacteria represent many of the existing antimicrobial drugs. Compared with other bacterial pathogens, direct preliminary screening by diffusion assays is a limiting factor against Mycobacterium tuberculosis (Mtb) and different methodologies have been used to improve the search for new molecules. However, the concern remains that most of the previously discovered molecules replicate by conventional procedures. The combination of multidisciplinary approaches with new technologies could advance the discovery of new leads against Mtb like considering the unexplored Actinobacteria jointly with selective and integrative procedures.

Planococcus Species - An Imminent Resource to Explore Biosurfactant and Bioactive Metabolites for Industrial Applications

The marine environment represents a well-off and diverse group of microbes, which offers an enormous natural bioactive compounds of commercial importance. These natural products have expanded rigorous awareness due to their widespread stability and functionality under harsh environmental conditions. The genus Planococcus is a halophilic bacterium known for the production of diverse secondary metabolites such as 2-acetamido-2-deoxy-α-d-glucopyranosyl-(1, 2)-β-d-fructofuranose exhibiting stabilizing effect and methyl glucosyl-3,4-dehydro-apo-8-lycopenoate displaying antioxidant activity. The genus Planococcus is reported generally for hydrocarbon degradation in comparison with biosurfactant/bioemulsifier secretion. Although Planococcus was proposed in 1894, it seized long stretch (till 1970) to get accommodated under the genus Planococcus authentically. Large-scale biosurfactant production from Planococcus was reported in 2014 with partial characterization. For the first time in 2019, we documented genomic and functional analysis of Planococcus sp. along with the physico-chemical properties of its biosurfactant. In 2020, again we screened biosurfactant for pharmacological applications. The present review discusses the comprehensive genomic insights and physical properties of Planococcus-derived biosurfactant. Moreover, we also highlight the prospects and challenges in biosurfactant production from Planococcus sp. Among ∼102 reports on biosurfactant produced by marine bacteria, 43 were of glycolipid and 59 were non-glycolipid type. Under other biosurfactant type, they were identified as lipopeptide (20) like surfactin (5), glycolipoprotein/lipoprotein (12), and other non-glycolipid (22). Planococcus sp. generally produces glycolipid-type biosurfactant (4) and exopolysaccharides (2). The single report documented in the literature is on biosurfactant production (glycolipid +non glycolipid) by diverse marine microbes (39) suggesting their novelty and diversity for biosurfactant secretion.

Recent developments in self-resistance gene directed natural product discovery

Covering: 2000 to 2019Natural products (NPs) are important sources of human therapeutic agents and pesticides. To prevent self-harm from bioactive NPs, some microbial producers employ self-resistance genes to protect themselves. One effective strategy is to employ a self-resistance enzyme (SRE), which is a slightly mutated version of the original metabolic enzyme, and is resistant to the toxic NP but is still functional. The presence of a SRE in a gene cluster can serve as a predictive window to the biological activity of the NPs synthesized by the pathway. In this highlight, we summarize representative examples of NP biosynthetic pathways that utilize self-resistance genes for protection. Recent discoveries based on self-resistance gene identification have helped in bridging the gap between activity-guided and genome-driven approaches for NP discovery and functional assignment.

Benwamycins A-G, Trialkyl-Substituted Benzene Derivatives from a Soil-Derived Streptomyces

Seven new trialkyl-substituted benzene derivatives named benwamycins A-G (1-7), together with three known congeners, 8-10, were isolated from culture broth of the soil-derived Streptomyces sp. KIB-H1471. Their structures were elucidated by using 1D and 2D NMR analyses in combination with HRESIMS data. The absolute configurations of 1-9 were determined by chemical conversion and comparison of circular dichroism spectra and confirmed for 1 by single-crystal X-ray crystallography. Compounds 6 and 7 have a unique γ-pyrone-like ring on one side chain. Compounds 2 and 6 inhibited human T cell proliferation with IC₅₀ values of 14.3 and 12.5 μM, respectively, without obvious cytotoxicity for naïve human T cells. Compounds 3 and 6 could weakly enhance insulin-stimulated glucose uptake.

Diversity, Ecology, and Prevalence of Antimicrobials in Nature

Microorganisms possess a variety of survival mechanisms, including the production of antimicrobials that function to kill and/or inhibit the growth of competing microorganisms. Studies of antimicrobial production have largely been driven by the medical community in response to the rise in antibiotic-resistant microorganisms and have involved isolated pure cultures under artificial laboratory conditions neglecting the important ecological roles of these compounds. The search for new natural products has extended to biofilms, soil, oceans, coral reefs, and shallow coastal sediments; however, the marine deep subsurface biosphere may be an untapped repository for novel antimicrobial discovery. Uniquely, prokaryotic survival in energy-limited extreme environments force microbial populations to either adapt their metabolism to outcompete or produce novel antimicrobials that inhibit competition. For example, subsurface sediments could yield novel antimicrobial genes, while at the same time answering important ecological questions about the microbial community.

Nocardiopsistins A-C: New angucyclines with anti-MRSA activity isolated from a marine sponge-derived Nocardiopsis sp. HB-J378

Marine natural products have become an increasingly important source of new drug leads during recent years. In an attempt to identify novel anti-microbial natural products by bioprospecting deep-sea Actinobacteria, three new angucyclines, nocardiopsistins A-C, were isolated from Nocardiopsis sp. strain HB-J378. Notably, the supplementation of the rare earth salt Lanthanum chloride (LaCl₃) during fermentation of HB-J378 significantly increased the yield of these angucyclines. The structures of nocardiopsistins A-C were identified by 1D and 2D NMR and HR-MS data. Nocardiopsistins A-C have activity against MRSA (methicillin-resistant Staphylococcus aureus) with MICs of 3.12–12.5 μg/mL; the potency of nocardiopsistin B is similar to that of the positive control, chloramphenicol. Bioinformatic analysis of the draft genome of HB-J378 identified a set of three core genes in a biosynthetic gene cluster that encode a typical aromatic or type II polyketide synthase (PKS) system, including ketoacyl:ACP synthase α-subunit (KS_α), β-subunit (KS_β) and acyl carrier protein (ACP). The production of nocardiopsistins A-C was abolished when the three genes were knocked out, indicating their indispensable role in the production of nocardiopsistins.

No Country for Old Worms: A Systematic Review of the Application of C. elegans to Investigate a Bacterial Source of Environmental Neurotoxicity in Parkinson's Disease

While progress has been made in discerning genetic associations with Parkinson's disease (PD), identifying elusive environmental contributors necessitates the application of unconventional hypotheses and experimental strategies. Here, we provide an overview of studies that we conducted on a neurotoxic metabolite produced by a species of common soil bacteria, Streptomyces venezuelae (S. ven), indicating that the toxicity displayed by this bacterium causes stress in diverse cellular mechanisms, such as the ubiquitin proteasome system and mitochondrial homeostasis. This dysfunction eventually leads to age and dose-dependent neurodegeneration in the nematode Caenorhabditis elegans. Notably, dopaminergic neurons have heightened susceptibility, but all of the neuronal classes eventually degenerate following exposure. Toxicity further extends to human SH-SY5Y cells, which also degenerate following exposure. Additionally, the neurons of nematodes expressing heterologous aggregation-prone proteins display enhanced metabolite vulnerability. These mechanistic analyses collectively reveal a unique metabolomic fingerprint for this bacterially-derived neurotoxin. In considering that epidemiological distinctions in locales influence the incidence of PD, we surveyed soils from diverse regions of Alabama, and found that exposure to ~30% of isolated Streptomyces species caused worm dopaminergic neurons to die. In addition to aging, one of the few established contributors to PD appears to be a rural lifestyle, where exposure to soil on a regular basis might increase the risk of interaction with bacteria producing such toxins. Taken together, these data suggest that a novel toxicant within the Streptomyces genus might represent an environmental contributor to the progressive neurodegeneration that is associated with PD.

Exploitation of Mangrove Endophytic Fungi for Infectious Disease Drug Discovery

There is an acute need for new and effective agents to treat infectious diseases. We conducted a screening program to assess the potential of mangrove-derived endophytic fungi as a source of new antibiotics. Fungi cultured in the presence and absence of small molecule epigenetic modulators were screened against Mycobacterium tuberculosis and the ESKAPE panel of bacterial pathogens, as well as two eukaryotic infective agents, Leishmania donovani and Naegleria fowleri. By comparison of bioactivity data among treatments and targets, trends became evident, such as the result that more than 60% of active extracts were revealed to be selective to a single target. Validating the technique of using small molecules to dysregulate secondary metabolite production pathways, nearly half (44%) of those fungi producing active extracts only did so following histone deacetylase inhibitory (HDACi) or DNA methyltransferase inhibitory (DNMTi) treatment.

Nonribosomal peptides and polyketides of Burkholderia: new compounds potentially implicated in biocontrol and pharmaceuticals

Bacteria belonging to the genus Burkholderia live in various ecological niches and present a significant role in the environments through the excretion of a wide variety of secondary metabolites including modular nonribosomal peptides (NRPs) and polyketides (PKs). These metabolites represent a widely distributed biomedically and biocontrol important class of natural products including antibiotics, siderophores, and anticancers as well as biopesticides that are considered as a novel source that can be used to defend ecological niche from competitors and to promote plant growth. The aim of this review is to present all NRPs produced or potentially produced by strains of Burkholderia, as NRPs represent a major source of active compounds implicated in biocontrol. The review is a compilation of results from a large screening we have performed on 48 complete sequenced genomes available in NCBI to identify NRPS gene clusters, and data found in the literature mainly because some interesting compounds are produced by strains not yet sequenced. In addition to NRPs, hybrids NRPs/PKs are also included. Specific features about biosynthetic gene clusters and structures of the modular enzymes responsible for the synthesis, the biological activities, and the potential uses in agriculture and pharmaceutical of NRPs and hybrids NRPs/PKs will also be discussed.

Bioprospecting Deep-Sea Actinobacteria for Novel Anti-infective Natural Products

The global prevalence of drug resistance has created an urgent need for the discovery of novel anti-infective drugs. The major source of antibiotics in current clinical practice is terrestrial actinobacteria; the less-exploited deep-sea actinobacteria may serve as an unprecedented source of novel natural products. In this study, we evaluated 50 actinobacteria strains derived from diverse deep water sponges and environmental niches for their anti-microbial activities against a panel of pathogens including Candida albicans, Clostridium difficile, Staphylococcus aureus, and methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa. More than half of the tested strains (27) were identified as active in at least one assay. The rare earth salt lanthanum chloride (LaCl₃) was shown to be as an effective elicitor. Among the 27 strains, the anti-microbial activity of 15 were induced or enhanced by the addition of LaCl₃. This part of study focused on one strain R818, in which potent antifungal activity was induced by the addition of LaCl₃. We found that the LaCl₃-activated metabolites in R818 are likely antimycin-type compounds. One of them, compound 1, has been purified. Spectroscopic analyses including HR-MS and 1D NMR indicated that this compound is urauchimycin D. The antifungal activity of compound 1 was confirmed with a minimal inhibitory concentration (MIC) of 25 μg/mL; the purified compound also showed a moderate activity against C. difficile. Additional notable strains are: strain N217 which showed both antifungal and antibacterial (including P. aeruginosa) activities and strain M864 which showed potent activity against C. difficile with an MIC value (0.125 μg/mL) lower than those of vancomycin and metronidazole. Our preliminary studies show that deep-sea actinobacteria is a promising source of anti-infective natural products.

A new actinomycin Z analogue with an additional oxygen bridge between chromophore and β-depsipentapeptide from Streptomyces sp. KIB-H714

Actinomycin Z₆ (1), a new member of the actinomycin family, along with three congeners of the Z-type (Z₁, Z₃, Z₅) actinomycins, are produced from Streptomyces sp. KIB-H714. Their structures were authenticated by comprehensive spectroscopic data interpretation. Different from all the reported Z-type actinomycins, the β-ring of the new compound actinomycin Z₆ includes an additional ring linked between the actinoyl chromophore and β-peptidolactone. In Z₃ and Z₅, the L-threonine in β-depsipeptide is replaced by the unusual 4-chlorothreonine, an amino acid rarely found in actinomycin family. All isolates were evaluated for cytotoxicity against five human tumor cell lines and for inhibitory activity against Candida albicans and Staphylococcus aureus.

Advancement of Biotechnology by Genetic Modifications

One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.

Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin

Advances in genomics and metabolomics have made clear in recent years that microbial biosynthetic capacities on Earth far exceed previous expectations. This is attributable, in part, to the realization that most microbial natural product (NP) producers harbor biosynthetic machineries not readily amenable to classical laboratory fermentation conditions. Such "cryptic" or dormant biosynthetic gene clusters (BGCs) encode for a vast assortment of potentially new antibiotics and, as such, have become extremely attractive targets for activation under controlled laboratory conditions. We report here that coculturing of a Rhodococcus sp. and a Micromonospora sp. affords keyicin, a new and otherwise unattainable bis-nitroglycosylated anthracycline whose mechanism of action (MOA) appears to deviate from those of other anthracyclines. The structure of keyicin was elucidated using high resolution MS and NMR technologies, as well as detailed molecular modeling studies. Sequencing of the keyicin BGC (within the Micromonospora genome) enabled both structural and genomic comparisons to other anthracycline-producing systems informing efforts to characterize keyicin. The new NP was found to be selectively active against Gram-positive bacteria including both Rhodococcus sp. and Mycobacterium sp. E. coli-based chemical genomics studies revealed that keyicin's MOA, in contrast to many other anthracyclines, does not invoke nucleic acid damage.

Mining of Microbial Genomes for the Novel Sources of Nitrilases

Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus, Sphingopyxis alaskensis, Saccharomonospora viridis, and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus, Nocardiopsis dassonvillei, Runella slithyformis, and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN) which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies.

Bluegenics: Bioactive Natural Products of Medicinal Relevance and Approaches to Their Diversification

Nature provides a valuable resource of medicinally relevant compounds, with many antimicrobial and antitumor agents entering clinical trials being derived from natural products. The generation of analogues of these bioactive natural products is important in order to gain a greater understanding of structure activity relationships; probing the mechanism of action, as well as to optimise the natural product's bioactivity and bioavailability. This chapter critically examines different approaches to generating natural products and their analogues, exploring the way in which synthetic and biosynthetic approaches may be blended together to enable expeditious access to new designer natural products.

-Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

Molecular Approaches to Screen Bioactive Compounds from Endophytic Fungi

Endophytic fungi are capable of producing plant associated metabolites and their analogs with therapeutic value. In order to identify the potential endophytic isolates producing bioactive compounds, one need to screen all isolated endophytes, which may run into hundreds. Isolation of endophytic fungi is relatively a simple process; but screening of the isolated fungi for required metabolite production is a cumbersome process. Endophytic fungi producing plant associated metabolites may contain genes involved in the entire biosynthetic pathway(s). Therefore, ascertaining the presence of key enzymes of a particular biosynthetic pathway could serve as a molecular marker for screening of these endophytes to produce that metabolite. In absence of entire biosynthetic pathways in endophytic fungi, plant genes associated with that metabolic pathway could serve as markers. This review focuses on the impact of molecular approaches to screen the endophytic fungi for the production of bioactive compounds. An attempt has been made on screening of anticancer compounds like taxol (paclitaxel), podophyllotoxin, and camptothecin using molecular markers. The advantages of molecular approaches over conventional methods to screen endophytic fungi and also identification of endophytic fungi are discussed.

RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression

Full-length RecE and RecT from Rac prophage mediate highly efficient linear-linear homologous recombination that can be used to clone large DNA regions directly from genomic DNA into expression vectors, bypassing library construction and screening. Homologous recombination mediated by Redαβ from lambda phage has been widely used for recombinant DNA engineering. Here we present a protocol for direct cloning and engineering of biosynthetic gene clusters, large operons or single genes from genomic DNA using one Escherichia coli host that harbors both RecET and Redαβ systems. The pipeline uses standardized cassettes for horizontal gene transfer options, as well as vectors with different replication origins configured to minimize recombineering background through the use of selectively replicating templates or CcdB counterselection. These optimized reagents and protocols facilitate fast acquisition of transgenes from genomic DNA preparations, which are ready for heterologous expression within 1 week.

Discovery of the New Plant Growth-Regulating Compound LYXLF2 Based on Manipulating the Halogenase in Amycolatopsis orientalis

Analysis of the Amycolatopsis orientalis HCCB10007 genome revealed new gene clusters involved in natural product biosynthesis that were not associated with the production of known compounds. Halogenases are a type of tailoring enzymes that are usually found within these secondary gene clusters. In this study, we identified an indole-type halometabolite 6-chrolo-1H-indole-3-carboxamide, named LYXLF2, by whole genome mining and metabolic profiling of a flavin-dependent halogenase mutant. LYXLF2 is a new plant growth-regulating compound that promotes root elongation. The results of this study demonstrated that the special gene knock-out/comparative metabolic profiling approach provides a powerful tool for the discovery of novel natural products by genome mining.

Elicitation of secondary metabolism in actinomycetes

Genomic sequence data have revealed the presence of a large fraction of putatively silent biosynthetic gene clusters in the genomes of actinomycetes that encode for secondary metabolites, which are not detected under standard fermentation conditions. This review focuses on the effects of biological (co-cultivation), chemical, as well as molecular elicitation on secondary metabolism in actinomycetes. Our review covers the literature until June 2014 and exemplifies the diversity of natural products that have been recovered by such approaches from the phylum Actinobacteria.

Biosynthetic potential-based strain prioritization for natural product discovery: a showcase for diterpenoid-producing actinomycetes

Natural products remain the best sources of drugs and drug leads and serve as outstanding small-molecule probes to dissect fundamental biological processes. A great challenge for the natural product community is to discover novel natural products efficiently and cost effectively. Here we report the development of a practical method to survey biosynthetic potential in microorganisms, thereby identifying the most promising strains and prioritizing them for natural product discovery. Central to our approach is the innovative preparation, by a two-tiered PCR method, of a pool of pathway-specific probes, thereby allowing the survey of all variants of the biosynthetic machineries for the targeted class of natural products. The utility of the method was demonstrated by surveying 100 strains, randomly selected from our actinomycete collection, for their biosynthetic potential of four classes of natural products, aromatic polyketides, reduced polyketides, nonribosomal peptides, and diterpenoids, identifying 16 talented strains. One of the talented strains, Streptomyces griseus CB00830, was finally chosen to showcase the discovery of the targeted classes of natural products, resulting in the isolation of three diterpenoids, six nonribosomal peptides and related metabolites, and three polyketides. Variations of this method should be applicable to the discovery of other classes of natural products.

Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A

Recent developments in next-generation sequencing technologies have brought recognition of microbial genomes as a rich resource for novel natural product discovery. However, owing to the scarcity of efficient procedures to connect genes to molecules, only a small fraction of secondary metabolomes have been investigated to date. Transformation-associated recombination (TAR) cloning takes advantage of the natural in vivo homologous recombination of Saccharomyces cerevisiae to directly capture large genomic loci. Here we report a TAR-based genetic platform that allows us to directly clone, refactor, and heterologously express a silent biosynthetic pathway to yield a new antibiotic. With this method, which involves regulatory gene remodeling, we successfully expressed a 67-kb nonribosomal peptide synthetase biosynthetic gene cluster from the marine actinomycete Saccharomonospora sp. CNQ-490 and produced the dichlorinated lipopeptide antibiotic taromycin A in the model expression host Streptomyces coelicolor. The taromycin gene cluster (tar) is highly similar to the clinically approved antibiotic daptomycin from Streptomyces roseosporus, but has notable structural differences in three amino acid residues and the lipid side chain. With the activation of the tar gene cluster and production of taromycin A, this study highlights a unique "plug-and-play" approach to efficiently gaining access to orphan pathways that may open avenues for novel natural product discoveries and drug development.

Microbial enzymes: tools for biotechnological processes

Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi.

Genome-guided discovery of diverse natural products from Burkholderia sp

Burkholderia species have emerged as a new source of diverse natural products. This mini-review covers all of the natural products discovered in recent years from Burkholderia sp. by genome-guided approaches--these refer to the use of bacterial genome sequence as an entry point for in silico structural prediction, wet lab experimental design, and execution. While reliable structural prediction based on cryptic biosynthetic gene cluster sequence was not always possible due to noncanonical domains and/or module organization of a deduced biosynthetic pathway, a molecular genetic method was often employed to detect or alter the expression level of the gene cluster to achieve an observable phenotype, which facilitated downstream natural product purification and identification. Those examples of natural product discovery from Burkholderia sp. provide practical guidance for future exploration of Gram-negative bacteria as a new source of natural products.

Medium optimization of Streptomyces sp. 17944 for tirandamycin B production and isolation and structural elucidation of tirandamycins H, I and J

We have recently isolated tirandamycin (TAM) B from Streptomyces sp. 17944 as a Brugia malayi AsnRS (BmAsnRS) inhibitor that efficiently kills the adult B. malayi parasites and does not exhibit general cytotoxicity to human hepatic cells. We now report (i) the comparison of metabolite profiles of S. sp. 17944 in six different media, (ii) identification of a medium enabling the production of TAM B as essentially the sole metabolite, and with improved titer, and (iii) isolation and structural elucidation of three new TAM congeners. These findings shed new insights into the structure-activity relationship of TAM B as a BmAsnRS inhibitor, highlighting the δ-hydroxymethyl-α,β-epoxyketone moiety as the critical pharmacophore, and should greatly facilitate the production and isolation of sufficient quantities of TAM B for further mechanistic and preclinical studies to advance the candidacy of TAM B as an antifilarial drug lead. The current study also serves as an excellent reminder that traditional medium and fermentation optimization should continue to be very effective in improving metabolite flux and titer.

Alternative sigma factor over-expression enables heterologous expression of a type II polyketide biosynthetic pathway in Escherichia coli

Background

Heterologous expression of bacterial biosynthetic gene clusters is currently an indispensable tool for characterizing biosynthetic pathways. Development of an effective, general heterologous expression system that can be applied to bioprospecting from metagenomic DNA will enable the discovery of a wealth of new natural products.

Methodology

We have developed a new Escherichia coli-based heterologous expression system for polyketide biosynthetic gene clusters. We have demonstrated the over-expression of the alternative sigma factor σ⁵⁴ directly and positively regulates heterologous expression of the oxytetracycline biosynthetic gene cluster in E. coli. Bioinformatics analysis indicates that σ⁵⁴ promoters are present in nearly 70% of polyketide and non-ribosomal peptide biosynthetic pathways.

Conclusions

We have demonstrated a new mechanism for heterologous expression of the oxytetracycline polyketide biosynthetic pathway, where high-level pleiotropic sigma factors from the heterologous host directly and positively regulate transcription of the non-native biosynthetic gene cluster. Our bioinformatics analysis is consistent with the hypothesis that heterologous expression mediated by the alternative sigma factor σ⁵⁴ may be a viable method for the production of additional polyketide products.

Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis

Secondary metabolites belonging to polyketide and nonribosomal peptide families constitute a major class of natural products with diverse biological functions and a variety of pharmaceutically important properties. Experimental studies have shown that the biosynthetic machinery for polyketide and nonribosomal peptides involves multi-functional megasynthases like Polyketide Synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) which utilize a thiotemplate mechanism similar to that for fatty acid biosynthesis. Availability of complete genome sequences for an increasing number of microbial organisms has provided opportunities for using in silico genome mining to decipher the secondary metabolite natural product repertoire encoded by these organisms. Therefore, in recent years there have been major advances in development of computational methods which can analyze genome sequences to identify genes involved in secondary metabolite biosynthesis and help in deciphering the putative chemical structures of their biosynthetic products based on analysis of the sequence and structural features of the proteins encoded by these genes. These computational methods for deciphering the secondary metabolite biosynthetic code essentially involve identification of various catalytic domains present in this PKS/NRPS family of enzymes; a prediction of various reactions in these enzymatic domains and their substrate specificities and also precise identification of the order in which these domains would catalyze various biosynthetic steps. Structural bioinformatics analysis of known secondary metabolite biosynthetic clusters has helped in formulation of predictive rules for deciphering domain organization, substrate specificity, and order of substrate channeling. In this chapter, the progress in development of various computational methods is discussed by different research groups, and specifically, the utility in identification of novel metabolites by genome mining and rational design of natural product analogs by biosynthetic engineering studies.