Oxytetracycline hyper-production through targeted genome reduction of Streptomyces rimosus

Most biosynthetic gene clusters (BGC) encoding the synthesis of important microbial secondary metabolites, such as antibiotics, are either silent or poorly expressed; therefore, to ensure a strong pipeline of novel antibiotics, there is a need to develop rapid and efficient strain development approaches. This study uses comparative genome analysis to instruct rational strain improvement, using Streptomyces rimosus, the producer of the important antibiotic oxytetracycline (OTC) as a model system. Sequencing of the genomes of two industrial strains M4018 and R6-500, developed independently from a common ancestor, identified large DNA rearrangements located at the chromosome end. We evaluated the effect of these genome deletions on the parental S. rimosus Type Strain (ATCC 10970) genome where introduction of a 145 kb deletion close to the OTC BGC in the Type Strain resulted in massive OTC overproduction, achieving titers that were equivalent to M4018 and R6-500. Transcriptome data supported the hypothesis that the reason for such an increase in OTC biosynthesis was due to enhanced transcription of the OTC BGC and not due to enhanced substrate supply. We also observed changes in the expression of other cryptic BGCs; some metabolites, undetectable in ATCC 10970, were now produced at high titers. This study demonstrated for the first time that the main force behind BGC overexpression is genome rearrangement. This new approach demonstrates great potential to activate cryptic gene clusters of yet unexplored natural products of medical and industrial value

Biološka kontrola sive plijesni Botrytis cinerea na grožđu s pomoću autohtonih vinskih kvasaca

Biocontrol activities of different yeast species and strains isolated from grape/must/wine environments have been compared to those of commercially available antagonistic yeast species of Candida oleophila. A total of 591 yeast isolates were tested in a preliminary screening on agar to select isolates showing inhibitory effect against Botrytis cinerea, the plant pathogen causing grey mould disease on grape. Yeast species Aureobasidium pullulans, Metschnikowia pulcherrima and Pichia guilliermondii showed, on average, higher biocontrol activity than commercially used yeast Candida oleophila. Furthermore, these three species and Saccharomyces cerevisiae, which is potentially interesting biocontrol agent against grey mould of grapes, were selected for their inhibitory effects and assayed in vitro on different solid synthetic media for their antagonistic capacity towards B. cinerea. The results indicate that the composition of the medium had an impact on the biocontrol activity of yeast species and strains, as Saccharomyces cerevisiae showed the highest antagonistic activity against B. cinerea when tested on media with increased concentrations of glucose. The antagonistic activity of selected yeast strains was finally determined on wounded and sound grape berries of cultivars Rebula and Chardonnay for their ability to inhibit infection by B. cinerea moulds. Results suggest that antagonist yeasts with the potential to control B. cinerea on grape can be found among the microflora associated with the berries.Ispitana je aktivnost različitih vrsta i sojeva kvasaca, izoliranih iz grožđa, mošta i vina, u sprečavanju bolesti grožđa, i to u usporedbi s komercijalnim kvascem Candida oleophila, koji djeluje kao antagonist. Na pločama agara preliminarno je ispitan 591 izolat kvasca radi odabira onih koji inhibiraju uzročnika sive plijesni na grožđu (Botrytis cinerea). Kvasci Aureobasidium pullulans, Metschnikowia pulcherrima i Pichia guilliermondii prosječno su imali veću aktivnost od kvasca Candida oleophila. Uzgojem in vitro na različitim sintetičkim podlogama proučena je mogućnost uporabe tih vrsta kvasaca, a i kvasca Saccharomyces cerevisiae, za biološko suzbijanje sive plijesni B. cinerea. Rezultati pokazuju da sastav podloge utječe na aktivnost kvasaca. Kvasac Saccharomyces cerevisiae u podlozi s povećanim udjelom glukoze imao je najizraženiji antagonistički učinak na B. cinerea. Ispitana je antagonistička aktivnost odabranih kvasaca na oštećenim i neoštećenim bobicama grožđa sorata Rebula i Chardonnay. Rezultati pokazuju da se iz prirodne mikrobne populacije grožđa mogu izdvojiti kvasci što imaju antagonistički učinak na sivu plijesan B. cinerea

Biocontrol of Grey Mould Disease on Grape Caused by Botrytis cinerea with Autochthonous Wine Yeasts

Biocontrol activities of different yeast species and strains isolated from grape/must/wine environments have been compared to those of commercially available antagonistic yeast species of Candida oleophila. A total of 591 yeast isolates were tested in a preliminary screening on agar to select isolates showing inhibitory effect against Botrytis cinerea, the plant pathogen causing grey mould disease on grape. Yeast species Aureobasidium pullulans, Metschnikowia pulcherrima and Pichia guilliermondii showed, on average, higher biocontrol activity than commercially used yeast Candida oleophila. Furthermore, these three species and Saccharomyces cerevisiae, which is potentially interesting biocontrol agent against grey mould of grapes, were selected for their inhibitory effects and assayed in vitro on different solid synthetic media for their antagonistic capacity towards B. cinerea. The results indicate that the composition of the medium had an impact on the biocontrol activity of yeast species and strains, as Saccharomyces cerevisiae showed the highest antagonistic activity against B. cinerea when tested on media with increased concentrations of glucose. The antagonistic activity of selected yeast strains was finally determined on wounded and sound grape berries of cultivars Rebula and Chardonnay for their ability to inhibit infection by B. cinerea moulds. Results suggest that antagonist yeasts with the potential to control B. cinerea on grape can be found among the microflora associated with the berries

Antiviral Activities of Halogenated Emodin Derivatives against Human Coronavirus NL63

The current COVID-19 outbreak has highlighted the need for the development of new vaccines and drugs to combat Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). Recently, various drugs have been proposed as potentially effective against COVID-19, such as remdesivir, infliximab and imatinib. Natural plants have been used as an alternative source of drugs for thousands of years, and some of them are effective for the treatment of various viral diseases. Emodin (1,3,8-trihydroxy-6-methylanthracene-9,10-dione) is a biologically active anthraquinone with antiviral activity that is found in various plants. We studied the selectivity of electrophilic aromatic substitution reactions on an emodin core (halogenation, nitration and sulfonation), which resulted in a library of emodin derivatives. The main aim of this work was to carry out an initial evaluation of the potential to improve the activity of emodin against human coronavirus NL63 (HCoV-NL63) and also to generate a set of initial SAR guidelines. We have prepared emodin derivatives which displayed significant anti-HCoV-NL63 activity. We observed that halogenation of emodin can improve its antiviral activity. The most active compound in this study was the iodinated emodin analogue E_3I, whose anti-HCoV-NL63 activity was comparable to that of remdesivir. Evaluation of the emodin analogues also revealed some unwanted toxicity to Vero cells. Since new synthetic routes are now available that allow modification of the emodin structure, it is reasonable to expect that analogues with significantly improved anti-HCoV-NL63 activity and lowered toxicity may thus be generatedWe thank the Slovenian Research Agency (P1-0134) and the APPLAUSE project for financial support to J.I. The APPLAUSE project is co-financed by the European Regional Development Fund through the Urban Innovative Actions (UIA) initiative. We also thank the Slovenian Research Agency (P4–0116) for financial support to H.P. The authors are grateful to the staff of The Centre for Research Infrastructure at the Faculty of Chemistry and Chemical Technology (IC UL FCCT).Peer reviewe

Antiviral activities of halogenated emodin derivatives against human coronavirus NL63

The current COVID-19 outbreak has highlighted the need for the development of new vaccines and drugs to combat Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). Recently, various drugs have been proposed as potentially effective against COVID-19, such as remdesivir, infliximab and imatinib. Natural plants have been used as an alternative source of drugs for thousands of years, and some of them are effective for the treatment of various viral diseases. Emodin (1,3,8-trihydroxy-6-methylanthracene-9,10-dione) is a biologically active anthraquinone with antiviral activity that is found in various plants. We studied the selectivity of electrophilic aromatic substitution reactions on an emodin core (halogenation, nitration and sulfonation), which resulted in a library of emodin derivatives. The main aim of this work was to carry out an initial evaluation of the potential to improve the activity of emodin against human coronavirus NL63 (HCoV-NL63) and also to generate a set of initial SAR guidelines. We have prepared emodin derivatives which displayed significant anti-HCoV-NL63 activity. We observed that halogenation of emodin can improve its antiviral activity. The most active compound in this study was the iodinated emodin analogue E_3I, whose anti-HCoV-NL63 activity was comparable to that of remdesivir. Evaluation of the emodin analogues also revealed some unwanted toxicity to Vero cells. Since new synthetic routes are now available that allow modification of the emodin structure, it is reasonable to expect that analogues with significantly improved anti-HCoV-NL63 activity and lowered toxicity may thus be generated

Oxytetracycline hyper-production through targeted genome reduction of Streptomyces rimosus

Most biosynthetic gene clusters (BGC) encoding the synthesis of important microbial secondary metabolites, such as antibiotics, are either silent or poorly expressedtherefore, to ensure a strong pipeline of novel antibiotics, there is a need to develop rapid and efficient strain development approaches. This study uses comparative genome analysis to instruct rational strain improvement, using Streptomyces rimosus, the producer of the important antibiotic oxytetracycline (OTC) as a model system. Sequencing of the genomes of two industrial strains M4018 and R6-500, developed independently from a common ancestor, identified large DNA rearrangements located at the chromosome end. We evaluated the effect of these genome deletions on the parental S. rimosus Type Strain (ATCC 10970) genome where introduction of a 145 kb deletion close to the OTC BGC in the Type Strain resulted in massive OTC overproduction, achieving titers that were equivalent to M4018 and R6-500. Transcriptome data supported the hypothesis that the reason for such an increase in OTC biosynthesis was due to enhanced transcription of the OTC BGC and not due to enhanced substrate supply. We also observed changes in the expression of other cryptic BGCssome metabolites, undetectable in ATCC 10970, were now produced at high titers. This study demonstrated for the first time that the main force behind BGC overexpression is genome rearrangement. This new approach demonstrates great potential to activate cryptic gene clusters of yet unexplored natural products of medical and industrial value

Multiple copies of the oxytetracycline gene cluster in selected Streptomyces rimosus strains can provide significantly increased titers.

Background: Natural products are a valuable source of biologically active compounds that have applications in medicine and agriculture. One disadvantage with natural products is the slow, time-consuming strain improvement regimes that are necessary to ensure sufficient quantities of target compounds for commercial production. Although great efforts have been invested in strain selection methods, many of these technologies have not been improved in decades, which might pose a serious threat to the economic and industrial viability of such important bioprocesses. Results: In recent years, introduction of extra copies of an entire biosynthetic pathway that encodes a target product in a single microbial host has become a technically feasible approach. However, this often results in minor to moderate increases in target titers. Strain stability and process reproducibility are the other critical factors in the industrial setting. Industrial Streptomyces rimosus strains for production of oxytetracycline are one of the most economically efficient strains ever developed, and thus these represent a very good industrial case. To evaluate the applicability of amplification of an entire gene cluster in a single host strain, we developed and evaluated various gene tools to introduce multiple copies of the entire oxytetracycline gene cluster into three different Streptomyces rimosus strains: wild-type, and medium and high oxytetracycline-producing strains. We evaluated the production levels of these engineered S. rimosus strains with extra copies of the oxytetracycline gene cluster and their stability, and the oxytetracycline gene cluster expression profiles; we also identified the chromosomal integration sites. Conclusions: This study shows that stable and reproducible increases in target secondary metabolite titers can be achieved in wild-type and in high oxytetracycline-producing strains, which always reflects the metabolic background of each independent S. rimosus strain. Although this approach is technically very demanding and requires systematic effort, when combined with modern strain selection methods, it might constitute a very valuable approach in industrial process development

Synthetic biology approaches to actinomycete strain improvement

Their biochemical versatility and biotechnological importance make actinomycete bacteria attractive targets for ambitious genetic engineering using the toolkit of synthetic biology. But their complex biology also poses unique challenges. This mini review discusses some of the recent advances in synthetic biology approaches from an actinomycete perspective and presents examples of their application to the rational improvement of industrially relevant strains