Streptomyces: host for refactoring of diverse bioactive secondary metabolites

Harnessing Biocontrol Potential of Streptomyces rochei Against Pythium aphanidermatum: Efficacy and Mechanisms

Tomato (Solanum lycopersicum) and chilli (Capsicum annuum) are globally significant vegetable crops susceptible to damping-off disease caused by Pythium aphanidermatum, leading to substantial yield losses. The study aimed to document the biocontrol and plant growth promotion potential of Streptomyces rochei against damping-off disease in tomato and chilli. The actinobacterial isolates ACS18 followed by ACT30, and AOE12 were accomplished as the most effective antagonists against P. aphanidermatum in vitro. Molecular characterization confirmed these isolates as members of Streptomyces genus, with ASH 18 the top performer identified as S. rochei isolate. Analysis of biomolecule through GC-MS during ditrophic interaction between pathogen and S. rochei showed the presence of various antifungal metabolites which were directly related to suppression of the pathogen. Subsequently, S. rochei was formulated into a talc-based preparation and used as seed treatment and soil application against damping-off. In greenhouse trials, significant reductions in damping-off incidence were observed, Furthermore, seedlings treated with S. rochei displayed enhanced root and shoot lengths compared to the uninoculated controls. These benefits potentiate S. rochei as a promising biocontrol agent and demonstrating its dual benefits of disease suppression and promotion of seedling growth.

Diversity of secondary metabolites from marine Streptomyces with potential anti-tubercular activity: a review

The bacterial genus Streptomyces is known for the prolific production of secondary metabolites, which exhibit remarkable structural diversity and potent biological activities. Tuberculosis (TB) remains a formidable global health challenge exacerbated by the emergence of antimicrobial resistance (AMR), necessitating the discovery of novel therapeutic agents. The untapped potential of marine Streptomyces-derived secondary metabolites offers a promising avenue for screening anti-tubercular (anti-TB) compounds with unique chemical structures and potential bioactive properties. The review emphasizes the diverse marine habitats and Streptomyces with novel anti-TB bioactive metabolites. It discusses fermentation and bioprocessing strategies for screening anti-TB drugs. This review also covers the chemical diversity, potency, mechanism of action, and structures of about seventy anti-TB compounds discovered from marine Streptomyces. These compounds span various chemical classes, including quinones, macrolactams, macrolides, phenols, esters, anthracyclines, peptides, glycosides, alkaloids, piperidones, thiolopyrrolones, nucleosides, terpenes, flavonoids, polyketides, and actinomycins. It emphasizes the need to explore marine ecosystems to discover more novel anti-TB natural products.

Mitigating genetic instability caused by the excision activity of the phiC31 integrase in Streptomyces

Over the past three decades, the integrase (Int) from Streptomyces phage phiC31 has become a valuable genome engineering tool across various species. phiC31 Int was thought to mediate unidirectional site-specific integration (attP × attB to attL and attR) in the absence of the phage-encoded recombination directionality factor (RDF). However, we have shown in this study that Int can also catalyze reverse excision (attL × attR to attP and attB) at low frequencies in Streptomyces lividans and Escherichia coli, causing genetic instability in engineered strains. To address this issue, we developed a two-plasmid co-conjugation (TPC) system. This system consists of an attP-containing integration vector and an Int expression suicide plasmid, both carrying oriT to facilitate efficient conjugation transfer from E. coli to Streptomyces. Using the TPC system, genetically stable integrants free of Int can be generated quickly and easily. The indigoidine-producing strains generated by the TPC system exhibited higher genetic stability and production efficiency compared to the indigoidine-producing strain generated by the conventional integration system, further demonstrating the utility of the TPC system in the field of biotechnology. We anticipate that the strategies presented here will be widely adopted for stable genetic engineering of industrial microbes using phage integrase-based integration systems.IMPORTANCELarge serine recombinases (LSRs), including the bacteriophage phiC31 integrase, were previously thought to allow only unidirectional site-specific integration (attP × attB to attL and attR). Our study is the first to show that the phiC31 integrase can also catalyze a low-efficiency reverse excision reaction in Streptomyces and E. coli without the involvement of the phage-encoded recombination directionality factor (RDF). The genetic instability caused by the low in vivo excisionase activity of the phiC31 integrase is a major challenge for biotechnological applications. Our study addresses this issue by developing a two-plasmid co-conjugation (TPC) system that facilitates the construction of Int-deficient genomic engineering strains. The Int-deficient integrants produced by this TPC system exhibit strong genetic stability for introduced genes and maintain stable production traits even in the absence of selection pressure, making them highly valuable for industrial applications.

Whole Genome Sequencing and Biocontrol Potential of Streptomyces luteireticuli ASG80 Against Phytophthora Diseases

Phytophthora-induced crop diseases, commonly known as "plant plagues", pose a significant threat to global food security. In this study, strain ASG80 was isolated from sisal roots and demonstrated a broad-spectrum antagonistic activity against several Phytophthora species and fungal pathogens. Strain ASG80 was identified as Streptomyces luteireticuli via phylogenetic analysis, digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI). Whole-genome sequencing identified 40 biosynthetic gene clusters (BGCs) related to secondary metabolite production, including antimicrobial compounds. Strain ASG80 extract exhibited broad-spectrum inhibitory activity against Phytophthora nicotianae, P. vignae, P. cinnamomi, and P. sojae. Pot experiments showed that strain ASG80 extract significantly reduced sisal zebra disease incidence, with an efficacy comparable to the fungicide metalaxyl. These findings suggest that strain ASG80 is a promising biocontrol agent with substantial potential for managing Phytophthora-related diseases in agriculture.

Bioactive Insecticides from Chemometric Diverse Ant-Associated Symbionts Streptomyces novaecaesareae and Streptomyces nojiriensis against the Fall Armyworm Larvae

The Streptomyces genus has long been recognized as a prolific and valuable source of diverse secondary metabolites. These metabolites contribute significantly to the intricate chemical diversity exhibited by Streptomyces, making them an indispensable reservoir for drug discovery, agricultural applications, and industrial processes. Exploiting the potential of these natural compounds holds the promise of ushering in a new era in insect pest management, reducing reliance on synthetic chemicals and fostering ecologically sustainable solutions. This study dives into the realm of chemo diversity within isolates of Streptomyces nojiriensis and Streptomyces novaecaesareae, with a specific focus on the production of insecticidal compounds. We explored chromatographic techniques for the identification and isolation of insecticidal compounds, and two bioactive compounds were identified in extracts of S. novaecaesareae. Valinomycin was identified from hexanic extracts of strain Asp59, while naphthomycin from ethyl acetate extracts of strain Asp58. These compounds showed insecticidal activity against first instars of Spodoptera frugiperda (Asp59: LC50 = 10.82 µg/µL, LC90 = 26.25 µg/µL; Asp58: LC50 = 15.05 µg/µL, LC90 = 38.84 µg/µL). Notably, this is the first report of naphthomycin as an insecticidal compound. The present study suggests that valinomycin and naphthomycin may be a novel biological source for the control of Spodoptera frugiperda in early stages.

First draft genome sequence data of TA4-1, the type strain of Gram-positive bacterium Streptomyces chiangmaiensis

TA4-1 is the type strain of Streptomyces chiangmaiensis. The TA4-1 strain was isolated from a stingless bee (Tetragonilla collina). Here we present the draft genome sequence data of S. chiangmaiensis TA4-1. The Illumina NextSeq 550 sequencer was used to generate paired-end reads from the genomic DNA of the pure culture of S. chiangmaiensis TA4-1. The draft genome sequence of strain TA4-1 consists of 776 contigs with a total size of 9,707,984 base pairs, an N50 of 32,937 base pairs, and a GC content of 69.73 %. Digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) analysis showed that S. yaanensis CGMCC 4.7035 had the highest dDDH value (32.7 %) and ANIm value (88.50 %) when compared with TA4-1. The presented data indicate the potential for a reference genome sequence in bacterial taxonomy, comparative genomics, and the investigation of bioactive compound biosynthesis in S. chiangmaiensis TA4-1. The draft genome sequence data have been deposited at NCBI under the Bioproject accession number PRJNA680432.

Escuzarmycins A-D, Potent Biofungicides to Control Septoria tritici Blotch

A study targeting novel antifungal metabolites identified potent in vitro antifungal activity against key plant pathogens in acetone extracts of Streptomyces sp. strain CA-296093. Feature-based molecular networking revealed the presence in this extract of antimycin-related compounds, leading to the isolation of four new compounds: escuzarmycins A-D (1-4). Extensive structural elucidation, employing 1D and 2D NMR, high-resolution mass spectrometry, Marfey's analysis, and NOESY correlations, confirmed their structures. The bioactivity of these compounds was tested against six fungal phytopathogens, and compounds 3 and 4 demonstrated strong efficacy, particularly against Zymoseptoria tritici, with compound 3 exhibiting the highest potency (EC50: 11 nM). Both compounds also displayed significant antifungal activity against Botrytis cinerea and Colletotrichum acutatum, with compound 4 proving to be the most potent. Despite moderate cytotoxicity against the human cancer cell line HepG2, compounds 3 and 4 emerge as promising fungicides for combating Septoria tritici blotch, anthracnose, and gray mold.

Analysis of the Anticancer Mechanism of OR3 Pigment from Streptomyces coelicolor JUACT03 Against the Human Hepatoma Cell Line Using a Proteomic Approach

This study assessed OR3 pigment, derived from Streptomyces coelicolor JUACT03, for its anticancer potential on HepG2 liver cancer cells and its safety on HEK293 normal cells. OR3 induced apoptosis and inhibited HepG2 cell proliferation, confirmed by caspase activation, Sub-G1 phase cell cycle arrest, and reduced colony formation. Proteomic analysis revealed altered expression of proteins associated with ribosomal function, mRNA processing, nuclear transport, proteasome activity, carbohydrate metabolism, chaperone function, histone regulation, and vesicle-mediated transport. Downregulation of proteins in MAPKAP kinase1, EIF2, mTOR, and EIF4 pathways contributed to apoptosis and cell cycle arrest. Changes in c-MYC, FUBP1 target proteins and upregulation of Prohibitin-1 (PHB1) were also noted. Western blot analysis supported alterations in eIF2, mTOR, and RAN pathways, including downregulation of RAB 5, c-MYC, p38, MAPK1, and MAPK3. OR3 exhibited significant anti-angiogenic activity in the in ovo CAM assay. In summary, OR3 demonstrated strong anticancer effects, inducing apoptosis, hindering proliferation, and displaying antiangiogenic properties. These findings highlight OR3's potential as an anticancer drug candidate, warranting further in vivo exploration.

Development of a group II intron-based genetic manipulation tool for Streptomyces

The availability of an alternative and efficient genetic editing technology is critical for fundamental research and strain improvement engineering of Streptomyces species, which are prolific producers of complex secondary metabolites with significant pharmaceutical activities. The mobile group II introns are retrotransposons that employ activities of catalytic intron RNAs and intron-encoded reverse transcriptase to precisely insert into DNA target sites through a mechanism known as retrohoming. We here developed a group II intron-based gene editing tool to achieve precise chromosomal gene insertion in Streptomyces. Moreover, by repressing the potential competition of RecA-dependent homologous recombination, we enhanced site-specific insertion efficiency of this tool to 2.38%. Subsequently, we demonstrated the application of this tool by screening and characterizing the secondary metabolite biosynthetic gene cluster (BGC) responsible for synthesizing the red pigment in Streptomyces roseosporus. Accompanied with identifying and inactivating this BGC, we observed that the impair of this cluster promoted cell growth and daptomycin production. Additionally, we applied this tool to activate silent jadomycin BGC in Streptomyces venezuelae. Overall, this work demonstrates the potential of this method as an alternative tool for genetic engineering and cryptic natural product mining in Streptomyces species.

Use of 3-Deoxy-D-arabino-heptulosonic acid 7-phosphate Synthase (DAHP Synthase) to Enhance the Heterologous Biosynthesis of Diosmetin and Chrysoeriol in an Engineered Strain of Streptomyces albidoflavus

Flavonoids are a large family of polyphenolic compounds with important agro-industrial, nutraceutical, and pharmaceutical applications. Among the structural diversity found in the flavonoid family, methylated flavonoids show interesting characteristics such as greater stability and improved oral bioavailability. This work is focused on the reconstruction of the entire biosynthetic pathway of the methylated flavones diosmetin and chrysoeriol in Streptomyces albidoflavus. A total of eight different genes (TAL, 4CL, CHS, CHI, FNS1, F3'H/CPR, 3'-OMT, 4'-OMT) are necessary for the heterologous biosynthesis of these two flavonoids, and all of them have been integrated along the chromosome of the bacterial host. The biosynthesis of diosmetin and chrysoeriol has been achieved, reaching titers of 2.44 mg/L and 2.34 mg/L, respectively. Furthermore, an additional compound, putatively identified as luteolin 3',4'-dimethyl ether, was produced in both diosmetin and chrysoeriol-producing strains. With the purpose of increasing flavonoid titers, a 3-Deoxy-D-arabino-heptulosonic acid 7-phosphate synthase (DAHP synthase) from an antibiotic biosynthetic gene cluster (BGC) from Amycolatopsis balhimycina was heterologously expressed in S. albidoflavus, enhancing diosmetin and chrysoeriol production titers of 4.03 mg/L and 3.13 mg/L, which is an increase of 65% and 34%, respectively. To the best of our knowledge, this is the first report on the de novo biosynthesis of diosmetin and chrysoeriol in a heterologous host.

An atypical two-component system, AtcR/AtcK, simultaneously regulates the biosynthesis of multiple secondary metabolites in Streptomyces bingchenggensis

Streptomyces bingchenggensis is an industrial producer of milbemycins, which are important anthelmintic and insecticidal agents. Two-component systems (TCSs), which are typically situated in the same operon and are composed of a histidine kinase and a response regulator, are the predominant signal transduction pathways involved in the regulation of secondary metabolism in Streptomyces. Here, an atypical TCS, AtcR/AtcK, in which the encoding genes (sbi_06838/sbi_06839) are organized in a head-to-head pair, was demonstrated to be indispensable for the biosynthesis of multiple secondary metabolites in S. bingchenggensis. With the null TCS mutants, the production of milbemycin and yellow compound was abolished but nanchangmycin was overproduced. Transcriptional analysis and electrophoretic mobility shift assays showed that AtcR regulated the biosynthesis of these three secondary metabolites by a MilR3-mediated cascade. First, AtcR was activated by phosphorylation from signal-triggered AtcK. Second, the activated AtcR promoted the transcription of milR3. Third, MilR3 specifically activated the transcription of downstream genes from milbemycin and yellow compound biosynthetic gene clusters (BGCs) and nanR4 from the nanchangmycin BGC. Finally, because NanR4 is a specific repressor in the nanchangmycin BGC, activation of MilR3 downstream genes led to the production of yellow compound and milbemycin but inhibited nanchangmycin production. By rewiring the regulatory cascade, two strains were obtained, the yield of nanchangmycin was improved by 45-fold to 6.08 g/L and the production of milbemycin was increased twofold to 1.34 g/L. This work has broadened our knowledge on atypical TCSs and provided practical strategies to engineer strains for the production of secondary metabolites in Streptomyces.IMPORTANCEStreptomyces bingchenggensis is an important industrial strain that produces milbemycins. Two-component systems (TCSs), which consist of a histidine kinase and a response regulator, are the predominant signal transduction pathways involved in the regulation of secondary metabolism in Streptomyces. Coupled encoding genes of TCSs are typically situated in the same operon. Here, TCSs with encoding genes situated in separate head-to-head neighbor operons were labeled atypical TCSs. It was found that the atypical TCS AtcR/AtcK played an indispensable role in the biosynthesis of milbemycin, yellow compound, and nanchangmycin in S. bingchenggensis. This atypical TCS regulated the biosynthesis of specialized metabolites in a cascade mediated via a cluster-situated regulator, MilR3. Through rewiring the regulatory pathways, strains were successfully engineered to overproduce milbemycin and nanchangmycin. To the best of our knowledge, this is the first report on atypical TCS, in which the encoding genes of RR and HK were situated in separate head-to-head neighbor operons, involved in secondary metabolism. In addition, data mining showed that atypical TCSs were widely distributed in actinobacteria.

Identification of Acetomycin as an Antifungal Agent Produced by Termite Gut-Associated Streptomycetes against Pyrrhoderma noxium

Plant fungal pathogen Pyrrhoderma noxium is responsible for the destructive and invasive disease of brown root rot currently affecting the city of Brisbane, Australia. In order to address this issue, environmentally friendly and safe alternatives to chemical control are preferred due to the city's public setting. Antifungal natural products are ideal candidates as biological control alternatives and can be detected through investigating the metabolomes of microbial symbionts. Within this study, an NMR-based metabolomics approach was applied to fermentation extracts obtained from 15 termite gut-associated streptomycetes. By analysing the NMR spectra, six of the extracts which displayed similar chemical profiles exhibited antifungal activity against the P. noxium pathogen. The major compound within these extracts was identified as acetomycin using NMR and X-ray crystallography analyses. This is the first reporting of acetomycin as a potential natural product fungicide, particularly as an antifungal agent against P. noxium. Inhibitory activity was also found against other important fungal crop pathogens, including Aspergillus niger, Botrytis cinerea, and Alteranaria alternata. Further experimentation using a woodblock test found inhibitory activity on the growth of the P. noxium pathogen for up to 3 weeks and a significant difference in the integrity of the woodblocks when conducting compression strength tests after 6 weeks. Therefore, acetomycin may be used as a biological control agent and natural product fungicide against P. noxium.

Metabolic engineering in Streptomyces albidoflavus for the biosynthesis of the methylated flavonoids sakuranetin, acacetin, and genkwanin

Flavonoids are important plant secondary metabolites showing antioxidant, antitumor, anti-inflammatory, and antiviral activities, among others. Methylated flavonoids are particularly interesting compared to non-methylated ones due to their greater stability and intestinal absorption, which improves their oral bioavailability. In this work we have stablished a metabolic engineered strain of Streptomyces albidoflavus with enhanced capabilities for flavonoid production, achieving a 1.6-fold increase in the biosynthesis of naringenin with respect to the parental strain. This improved strain, S. albidoflavus UO-FLAV-004, has been used for the heterologous biosynthesis of the methylated flavonoids sakuranetin, acacetin and genkwanin. The achieved titers of sakuranetin and acacetin were 8.2 mg/L and 5.8 mg/L, respectively. The genkwanin titers were 0.8 mg/L, with a bottleneck identified in this producing strain. After applying a co-culture strategy, genkwanin production titers reached 3.5 mg/L, which represents a 4.4-fold increase. To our knowledge, this study presents the first biosynthesis of methylated flavonoids in not only any Streptomyces species, but also in any Gram-positive bacteria.

Isolation, Characterization of Pyraclostrobin Derived from Soil Actinomycete Streptomyces sp. HSN-01 and Its Antimicrobial and Anticancer Activity

The present study demonstrated the isolation, characterization, and antimicrobial and anticancer activity of active metabolite produced from mining-soil-derived actinomycetes. Among the 21 actinomycete isolates, the isolate HSN-01 exhibited significant antimicrobial activity in primary screening and was identified as Streptomyces sp. through 16S rRNA gene sequencing. The active metabolite was separated, purified, and confirmed through UV-Vis spectroscopy, FTIR, HR-ESI-MS, and NMR analysis and identified as pyraclostrobin. Further, the active metabolite pyraclostrobin was tested for antimicrobial and anticancer activity against the hepatocellular carcinoma (HepG2) cell line. The metabolite exhibited maximum antimicrobial potential with 17.0, 13.33, 17.66, 15.66, 14.66, and 14.0 mm of inhibition against B. cereus, S. aureus, E. coli, P. aeruginosa, S. flexneri, and C. glabrata. The active metabolite exhibited dose-dependent anticancer potential against the hepatocellular carcinoma (HepG2) cell line with the IC₅₀ 56.76 µg/mL. This study suggests that Streptomyces sp. HSN-01 is an excellent source of active secondary metabolites with various biological activities.

Streptomyces: The biofactory of secondary metabolites

Natural products derived from microorganisms serve as a vital resource of valuable pharmaceuticals and therapeutic agents. Streptomyces is the most ubiquitous bacterial genus in the environments with prolific capability to produce diverse and valuable natural products with significant biological activities in medicine, environments, food industries, and agronomy sectors. However, many natural products remain unexplored among Streptomyces. It is exigent to develop novel antibiotics, agrochemicals, anticancer medicines, etc., due to the fast growth in resistance to antibiotics, cancer chemotherapeutics, and pesticides. This review article focused the natural products secreted by Streptomyces and their function and importance in curing diseases and agriculture. Moreover, it discussed genomic-driven drug discovery strategies and also gave a future perspective for drug development from the Streptomyces.

Plant Natural Products as Antimicrobials for Control of Streptomyces scabies: A Causative Agent of the Common Scab Disease

The common scab disease caused by Streptomyces scabies, a soil-dwelling Gram-positive bacterium, is an economically important disease of potatoes and other tuber crops. The lack of effective treatments against this disease accounts for large economic losses globally. Plant extracts were screened to find several that effectively inhibited Streptomyces scabies growth in culture. Seven tinctures showed the greatest inhibition of S. scabies growth by reducing pathogen growth in culture by 75% or more. These extracts were myrrh, garlic, cayenne, barberry, frankincense, wild indigo root, and lavender. Myrrh extract from Commiphora myrrha, a resin made from tree sap, showed strong antibacterial activity by reducing the growth of S. scabies to 13% of the control. Additionally, a flavonoid library was screened to identify several compounds that were effective to control the pathogen growth. The flavonoids that showed the greatest inhibition of Streptomyces scabies growth were sophoraflavanone G, jaceosidin, baicalein, and quercetin. Minimum inhibitory concentrations for the effective flavonoids were calculated to be 6.8 ± 0.4 μM, 100.0 ± 2.1 μM, 202.9 ± 5.3 μM, and 285.2 ± 6.8 μM, respectively. The mean lethal doses for these flavonoids against Streptomyces scabies were 2.0 ± 0.1 μM, 22.6 ± 0.5 μM, 52.9 ± 1.3 μM, and 37.8 ± 1.0 μM, respectively. A live/dead assay showed complete cell death in the presence of sophoraflavanone G indicative of a bactericidal mechanism for flavonoid action on Streptomyces scabies. Scanning electron and transmission electron microscopy imaging showed damaged cell membrane morphologies when Streptomyces scabies was exposed to these flavonoids. Mycelia appeared as flat and deflated structures with contents seen as spewing from branching hyphae with numerous holes and tears in the membrane structure indicative of cell death. Sophoraflavanone G showed the greatest potency and potential as a natural antibiotic from the library of tested flavonoids. These results suggest that these plant compounds act on the pathogen through a bactericidal mechanism involving cell membrane destabilization and disruption leading to cell death.

Streptomyces as Microbial Chassis for Heterologous Protein Expression

Heterologous production of recombinant proteins is gaining increasing interest in biotechnology with respect to productivity, scalability, and wide applicability. The members of genus Streptomyces have been proposed as remarkable hosts for heterologous production due to their versatile nature of expressing various secondary metabolite biosynthetic gene clusters and secretory enzymes. However, there are several issues that limit their use, including low yield, difficulty in genetic manipulation, and their complex cellular features. In this review, we summarize rational engineering approaches to optimizing the heterologous production of secondary metabolites and recombinant proteins in Streptomyces species in terms of genetic tool development and chassis construction. Further perspectives on the development of optimal Streptomyces chassis by the design-build-test-learn cycle in systems are suggested, which may increase the availability of secondary metabolites and recombinant proteins.