scholarly journals Adrenaline-mediated activation of antibiotic production in Streptomyces highlights catechol as elicitor of specialized metabolism

2021 ◽  
Author(s):  
Gilles van Wezel ◽  
Doris van Bergeijk ◽  
Somayah Elsayed ◽  
Chao Du ◽  
Isabel Nunez Santiago ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Gene Clusters ◽  
Bioactive Molecules ◽  
Stress Hormone ◽  
Biosynthetic Gene Clusters ◽  
Mass Spectral ◽  
Catechol 1,2 Dioxygenase ◽  
Human Stress ◽  
First Time ◽  
Catechol Moiety

Abstract Actinobacteria are a rich source of bioactive molecules, and genome sequencing has shown that the vast majority of their biosynthetic potential has yet to be explored. However, many of their biosynthetic gene clusters (BGCs) are poorly expressed in the laboratory, which prevents discovery of their cognate natural products. To exploit their full biosynthetic potential, better understanding of the signals that promote the expression of BGCs is needed. Here, we show that the human stress hormone epinephrine (adrenaline) elicits antibiotic production by Actinobacteria. Catechol was established as the likely eliciting moiety, since similar responses were seen for catechol and for the catechol-containing molecules dopamine and catechin but not for related molecules. Exploration of the catechol-responsive strain Streptomyces sp. MBT84 using mass spectral networking revealed elicitation of a BGC that produces the angucycline glycosides aquayamycin, urdamycinone B and galtamycin C. Heterologous expression of the catechol-cleaving enzymes catechol 1,2-dioxygenase or catechol 2,3 dioxygenase counteracted the eliciting effect of catechol. Thus, for the first time we show the activation of natural product biosynthesis by a human hormone, leading to the identification of the ubiquitous catechol moiety as elicitor of BGCs for siderophores and antibiotics.

scholarly journals Microbiological and molecular insights on rare Actinobacteria harboring bioactive prospective

2020 ◽  
Vol 44 (1) ◽  
Author(s):  
Dina H. Amin ◽  
Nagwa A. Abdallah ◽  
Assem Abolmaaty ◽  
Sahar Tolba ◽  
Elizabeth M. H. Wellington
Keyword(s):  
Bioinformatics Analysis ◽  
Genetic Manipulation ◽  
Antibiotic Production ◽  
Gene Clusters ◽  
Bioactive Molecules ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Pcr Screening ◽  
Molecular Approaches ◽  
Shed Light

Abstract Background Actinobacteria is as a group of advanced filamentous bacteria. Rare Actinobacteria are of special interest as they are rarely isolated from the environments. They are a major source of important bioactive compounds. Determining the proper strategy for the identification of Actinobacteria harboring biosynthetic gene clusters and producing bioactive molecules is a challenging platform. Methodology In this review, we discuss a consequence of microbiological and molecular methods for the identification of rare Actinobacteria. In addition to that, we shed light on rare Actinobacteria’s significance in antibiotic production. We also clarified molecular approaches for the manipulation of novel biosynthetic gene clusters via PCR screening, fosmid libraries, and Illumina whole-genome sequencing in combination with bioinformatics analysis. Conclusion Perceptions of the conventional and molecular identification of Actinobacteria were conducted. This will open the door for the genetic manipulation of novel antibiotic gene clusters in heterologous hosts. Also, these conclusions will lead to constructing new bioactive molecules via genetically engineering biosynthetic pathways.

Biosynthetic strategies for tetramic acid formation

2021 ◽  
Author(s):  
Xuhua Mo ◽  
Tobias A. M. Gulder
Keyword(s):  
Molecular Mechanism ◽  
Gene Clusters ◽  
Acid Formation ◽  
Biosynthetic Gene ◽  
Tetramic Acid ◽  
Biosynthetic Gene Clusters ◽  
The Individual ◽  
First Time ◽  
Acid Unit

Over 30 biosynthetic gene clusters for natural tetramate have been identified. This highlight reviews the biosynthetic strategies for formation of tetramic acid unit for the first time, discussing the individual molecular mechanism in detail.

scholarly journals Identification of a New Antimicrobial, Desertomycin H, Utilizing a Modified Crowded Plate Technique

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 424
Author(s):  
Osama G. Mohamed ◽  
Sadaf Dorandish ◽  
Rebecca Lindow ◽  
Megan Steltz ◽  
Ifrah Shoukat ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Gene Clusters ◽  
Multidrug Resistant ◽  
Microbial Interactions ◽  
Mass Spectrometry Data ◽  
Metagenomic Data ◽  
Resistant Bacteria ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Plate Technique

The antibiotic-resistant bacteria-associated infections are a major global healthcare threat. New classes of antimicrobial compounds are urgently needed as the frequency of infections caused by multidrug-resistant microbes continues to rise. Recent metagenomic data have demonstrated that there is still biosynthetic potential encoded in but transcriptionally silent in cultivatable bacterial genomes. However, the culture conditions required to identify and express silent biosynthetic gene clusters that yield natural products with antimicrobial activity are largely unknown. Here, we describe a new antibiotic discovery scheme, dubbed the modified crowded plate technique (mCPT), that utilizes complex microbial interactions to elicit antimicrobial production from otherwise silent biosynthetic gene clusters. Using the mCPT as part of the antibiotic crowdsourcing educational program Tiny Earth®, we isolated over 1400 antibiotic-producing microbes, including 62, showing activity against multidrug-resistant pathogens. The natural product extracts generated from six microbial isolates showed potent activity against vancomycin-intermediate resistant Staphylococcus aureus. We utilized a targeted approach that coupled mass spectrometry data with bioactivity, yielding a new macrolactone class of metabolite, desertomycin H. In this study, we successfully demonstrate a concept that significantly increased our ability to quickly and efficiently identify microbes capable of the silent antibiotic production.

scholarly journals Phytoplankton trigger the production of cryptic metabolites in the marine actinobacteria Salinispora tropica

2020 ◽  
Author(s):  
Audam Chhun ◽  
Despoina Sousoni ◽  
Maria del Mar Aguiló-Ferretjans ◽  
Lijiang Song ◽  
Christophe Corre ◽  
...  
Keyword(s):  
Natural Products ◽  
Secondary Metabolites ◽  
Antibiotic Production ◽  
Antimicrobial Effect ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Marine Actinobacteria ◽  
Salinispora Tropica ◽  
Eukaryotic Phytoplankton

AbstractBacteria from the Actinomycete family are a remarkable source of natural products with pharmaceutical potential. The discovery of novel molecules from these organisms is, however, hindered because most of the biosynthetic gene clusters (BGCs) encoding these secondary metabolites are cryptic or silent and are referred to as orphan BGCs. While co-culture has proven to be a promising approach to unlock the biosynthetic potential of many microorganisms by activating the expression of these orphan BGCs, it still remains an underexplored technique. The marine actinobacteria Salinispora tropica, for instance, produces valuable compounds such as the anti-cancer molecule salinosporamide A but half of its putative BGCs are still orphan. Although previous studies have looked into using marine heterotrophs to induce orphan BGCs in Salinispora, the potential impact of co-culturing marine phototrophs with Salinispora has yet to be investigated. Following the observation of clear antimicrobial phenotype of the actinobacterium on a range of phytoplanktonic organisms, we here report the discovery of novel cryptic secondary metabolites produced by S. tropica in response to its co-culture with photosynthetic primary producers. An approach combining metabolomics and proteomics revealed that the photosynthate released by phytoplankton influences the biosynthetic capacities of S. tropica with both production of new molecules and the activation of orphan BGCs. Our work pioneers the use of phototrophs as a promising strategy to accelerate the discovery of novel natural products from actinobacteria.ImportanceThe alarming increase of antimicrobial resistance has generated an enormous interest in the discovery of novel active compounds. The isolation of new microbes to untap novel natural products is currently hampered because most biosynthetic gene clusters (BGC) encoded by these microorganisms are not expressed under standard laboratory conditions, i.e. mono-cultures. Here we show that co-culturing can be an easy way for triggering silent BGC. By combining state-of-the-art metabolomics and high-throughput proteomics, we characterized the activation of cryptic metabolites and silent biosynthetic gene clusters in the marine actinobacteria Salinispora tropica by the presence of phytoplankton photosynthate. We further suggest a mechanistic understanding of the antimicrobial effect this actinobacterium has on a broad range of prokaryotic and eukaryotic phytoplankton species and reveal a promising candidate for antibiotic production.

scholarly journals Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool

2018 ◽  
Author(s):  
Javier Santos-Aberturas ◽  
Govind Chandra ◽  
Luca Frattaruolo ◽  
Rodney Lacret ◽  
Thu H. Pham ◽  
...  
Keyword(s):  
Genome Mining ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Bioactive Molecules ◽  
Post Translational Modification ◽  
Biosynthetic Gene Clusters ◽  
New Family ◽  
The Family ◽  
Modified Peptides ◽  
Mining Tool

ABSTRACTThe rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be a rare post-translational modification, which is catalyzed by a pair of proteins (YcaO and TfuA) in Archaea. In Actinobacteria, the thioviridamide-like molecules are a family of cytotoxic RiPPs that feature multiple thioamides, and it has been proposed that a YcaO-TfuA pair of proteins also catalyzes their formation. Potential biosynthetic gene clusters encoding YcaO and TfuA protein pairs are common in Actinobacteria but the chemical diversity generated by these pathways is almost completely unexplored. A RiPPER analysis reveals a highly diverse landscape of precursor peptides encoded in previously undescribed gene clusters that are predicted to make thioamidated RiPPs. To illustrate this strategy, we describe the first rational discovery of a new family of thioamidated natural products, the thiovarsolins from Streptomyces varsoviensis.

scholarly journals Modular and Integrative Vectors for Synthetic Biology Applications in Streptomyces spp.

2019 ◽  
Vol 85 (16) ◽  
Author(s):  
Céline Aubry ◽  
Jean-Luc Pernodet ◽  
Sylvie Lautru
Keyword(s):  
Synthetic Biology ◽  
Anticancer Agents ◽  
Gene Clusters ◽  
Bioactive Molecules ◽  
Dna Assembly ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Dna Cloning ◽  
Specialized Metabolism ◽  
Assembly Method

ABSTRACT With the development of synthetic biology in the field of (actinobacterial) specialized metabolism, new tools are needed for the design or refactoring of biosynthetic gene clusters. If libraries of synthetic parts (such as promoters or ribosome binding sites) and DNA cloning methods have been developed, to our knowledge, not many vectors designed for the flexible cloning of biosynthetic gene clusters have been constructed. We report here the construction of a set of 12 standardized and modular vectors designed to afford the construction or the refactoring of biosynthetic gene clusters in Streptomyces species, using a large panel of cloning methods. Three different resistance cassettes and four orthogonal integration systems are proposed. In addition, FLP recombination target sites were incorporated to allow the recycling of antibiotic markers and to limit the risks of unwanted homologous recombination in Streptomyces strains when several vectors are used. The functionality and proper integration of the vectors in three commonly used Streptomyces strains, as well as the functionality of the Flp-catalyzed excision, were all confirmed. To illustrate some possible uses of our vectors, we refactored the albonoursin gene cluster from Streptomyces noursei using the BioBrick assembly method. We also used the seamless ligase chain reaction cloning method to assemble a transcription unit in one of the vectors and genetically complement a mutant strain. IMPORTANCE One of the strategies employed today to obtain new bioactive molecules with potential applications for human health (for example, antimicrobial or anticancer agents) is synthetic biology. Synthetic biology is used to biosynthesize new unnatural specialized metabolites or to force the expression of otherwise silent natural biosynthetic gene clusters. To assist the development of synthetic biology in the field of specialized metabolism, we constructed and are offering to the community a set of vectors that were intended to facilitate DNA assembly and integration in actinobacterial chromosomes. These vectors are compatible with various DNA cloning and assembling methods. They are standardized and modular, allowing the easy exchange of a module by another one of the same nature. Although designed for the assembly or the refactoring of specialized metabolite gene clusters, they have a broader potential utility, for example, for protein production or genetic complementation.

scholarly journals Competition sensing alters antibiotic production in Streptomyces

2020 ◽  
Author(s):  
Sanne Westhoff ◽  
Alexander Kloosterman ◽  
Stephan F. A. van Hoesel ◽  
Gilles P. van Wezel ◽  
Daniel E. Rozen
Keyword(s):  
Genetic Relatedness ◽  
Cell Damage ◽  
Antibiotic Production ◽  
Interference Competition ◽  
Resource Limitation ◽  
Gene Clusters ◽  
Regulatory Control ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
The Social

ABSTRACTOne of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require “elicitors” to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing streptomycetes we show that inhibition between competitors is common and occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreased in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competion. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes.SIGNIFICANCE STATEMENTBacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production in Streptomyces, bacteria renowned for their production of antibiotics. We show that Streptomyces are more likely to produce antibiotics when grown with closely related competitors or that share biosynthetic pathways for secondary metabolites, but not when they are threatened by competitor’s toxins, in contrast to predictions of the competition sensing hypothesis. Streptomyces also often reduce their output of antibiotics when grown with competitors, especially under nutrient limitation. Our findings highlight that interactions between the social and resource environments strongly regulate antibiotic production in these medicinally important bacteria.

scholarly journals Genome Sequences of Serratia Strains Revealed Common Genes in Both Serratomolides Gene Clusters

Biology ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 482
Author(s):  
Catarina Marques-Pereira ◽  
Diogo Neves Proença ◽  
Paula V. Morais
Keyword(s):  
Comparative Genomics ◽  
Gene Cluster ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Genome Sequences ◽  
Biosynthetic Gene Clusters ◽  
Bacteria And Fungi ◽  
Different Strains ◽  
First Time

Serratia strains are ubiquitous microorganisms with the ability to produce serratomolides, such as serrawettins. These extracellular lipopeptides are described as biocides against many bacteria and fungi and may have a nematicidal activity against phytopathogenic nematodes. Serrawettins W1 and W2 from different strains have different structures that might be correlated with distinct genomic organizations. This work used comparative genomics to determine the distribution and the organization of the serrawettins biosynthetic gene clusters in all the 84 publicly available genomes of the Serratia genus. The serrawettin W1 and W2 gene clusters’ organization was established using antiSMASH software and compared with single and short data previously described for YD25TSerratia. Here, the serrawettin W1 gene clusters’ organization is reported for the first time. The serrawettin W1 biosynthetic gene swrW was present in 17 Serratia genomes. Eighty different coding sequence (CDS) were assigned to the W1 gene cluster, 13 being common to all clusters. The serrawettin W2 swrA gene was present in 11 Serratia genomes. The W2 gene clusters included 68 CDS with 24 present in all the clusters. The genomic analysis showed the swrA gene constitutes five modules, four with three domains and one with four domains, while the swrW gene constitutes one module with four domains. This work identified four genes common to all serrawettin gene clusters, highlighting their essential potential in the serrawettins biosynthetic process.

scholarly journals Endophytic microbes from Nigerian ethnomedicinal plants: a potential source for bioactive secondary metabolites—a review

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Chijioke E. Ezeobiora ◽  
Nwamaka H. Igbokwe ◽  
Dina H. Amin ◽  
Udoma E. Mendie
Keyword(s):  
Infectious Diseases ◽  
Anticancer Agents ◽  
Gene Clusters ◽  
Emerging Diseases ◽  
Bioactive Molecules ◽  
Main Body ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Ethnomedicinal Plants ◽  
Bacteria And Fungi

Abstract Background Endophytes are highly beneficial species of microbes that live in symbiosis with plant tissues in the setting. Endophytes are difficult to isolate in their natural environment, and they are understudied despite being a rich source of bioactive molecules. There are varieties of new infectious diseases emerging across the world, necessitating a constant and expanded search for newer and more efficient bioactive molecules. Nigeria is known for its biodiversity in ethnomedicinal plants, yet these plants are understudied for endophytic microbes harbouring novel bioactive molecules. Main body Endophytes are a source of novel organic natural molecules and are thought to be drug discovery frontiers. Endophyte research has contributed to the discovery of possible anticancer agents following the discovery of taxol. Endophyte research has contributed to the discovery of possible drug compounds with antimicrobial, antioxidant, antiviral, antidiabetic, anti-Alzheimers disease and immunosuppressive properties among others. These breakthroughs provide hope for combating incurable diseases, drug resistance, the emergence of new infectious diseases, and other human health issues. Finding new medicines that may be effective candidates for treating newly emerging diseases in humans has a lot of promise. Most studies have been on fungi endophytes, with just a few reports on bacterial endophytes. The biology of endophytic bacteria and fungi, as well as endophytic microbes isolated from Nigerian medicinal plants, their isolation methods, identification by morphological and molecular methods, fermentation, purification, identification of bioactive compounds and biosynthetic gene clusters are all covered in this study. Conclusion In Nigeria, the sourcing and isolation of endophytes harboring biosynthetic gene clusters are still understudied, necessitating a rigorous quest for bioactive molecules in endophytes inhabiting various ethnomedicinal plants.

scholarly journals The Antibiotic Andrimid Produced by Vibrio coralliilyticus Increases Expression of Biosynthetic Gene Clusters and Antibiotic Production in Photobacterium galatheae

2020 ◽  
Vol 11 ◽  
Author(s):  
Yannick Buijs ◽  
Thomas Isbrandt ◽  
Sheng-Da Zhang ◽  
Thomas Ostenfeld Larsen ◽  
Lone Gram
Keyword(s):  
Stress Response ◽  
Antibiotic Production ◽  
Gene Clusters ◽  
Multidrug Resistant ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Gene Encoding ◽  
Chemical Measurements ◽  
Low Concentrations ◽  
Vibrio Coralliilyticus

The development and spread of multidrug resistant pathogens have reinforced the urgency to find novel natural products with antibiotic activity. In bacteria, orphan biosynthetic gene clusters (BGCs) far outnumber the BGCs for which chemistry is known, possibly because they are transcriptionally silent under laboratory conditions. A strategy to trigger the production of this biosynthetic potential is to challenge the microorganism with low concentrations of antibiotics, and by using a Burkholderia genetic reporter strain (Seyedsayamdost, Proc Natl Acad Sci 111:7266–7271), we found BGC unsilencing activity for the antimicrobial andrimid, produced by the marine bacterium Vibrio coralliilyticus. Next, we challenged another marine Vibrionaceae, Photobacterium galatheae, carrier of seven orphan BGCs with sub-inhibitory concentrations of andrimid. A combined approach of transcriptional and chemical measurements of andrimid-treated P. galatheae cultures revealed a 10-fold upregulation of an orphan BGC and, amongst others, a 1.6–2.2-fold upregulation of the gene encoding the core enzyme for biosynthesis of holomycin. Also, addition of andrimid caused an increase, based on UV-Vis peak area, of 4-fold in production of the antibiotic holomycin. Transcriptional measurements of stress response related genes in P. galatheae showed a co-occurrence of increased transcript levels of rpoS (general stress response) and andrimid induced holomycin overproduction, while in trimethoprim treated cultures attenuation of holomycin production coincided with a transcriptional increase of recA (SOS stress response). This study shows that using antimicrobial compounds as activators of secondary metabolism can be a useful strategy in eliciting biosynthetic gene clusters and facilitate natural product discovery. Potentially, such interactions could also have ecological relevant implications.

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