Biology subjects

Elsayed, S. S.

Publications and source records attributed to Elsayed, S. S..

11 recordsLinked to original sources

bioRxiv2026

Plant-associated Streptomyces detoxify the mycotoxin fusaric acid by amino acid conjugation

Streptomycetes are prevalent members of soil and plant microbiomes, yet how they cope with toxins produced by root-infecting fungal pathogens remains poorly understood. Plant pathogenic Fusarium species produce the mycotoxin fusaric acid (FA) that contributes to virulence and perturbs rhizosphere microbiome dynamics. Here, we show that root-colonising Streptomyces sp. ATMOS43 neutralizes FA through amino acid conjugation. Metabolomics revealed the formation of single amino acid and dipeptidyl conjugates of FA, with FA-Ser as a major conjugate that lacked detectable toxicity in in vitro and in planta assays. Proteomics and physiological analyses revealed that FA toxicity involves, in part, zinc chelation, which is abolished upon conjugation of FA to Ser. Co-cultivation experiments further showed that Streptomyces sp. ATMOS43 restores growth of FA-sensitive streptomycetes, indicating that conjugation can mitigate the impact of FA on plant microbiome assembly. Together, our findings show that plant-associated streptomycetes can protect plants by directly inhibiting Fusarium growth and by neutralizing its toxic virulence factor FA.

microbiology↗

bioRxiv2026

Reconstructing plant beneficial bacterial consortia by integrating dilution-to-extinction microbiome perturbation with genome-resolved synthetic ecology

Across the biosphere, microbiomes play essential roles in shaping the health of their host. One notable example of such a microbiome-associated phenotype is disease-suppressive soils, where susceptible plant hosts enrich and activate specific rhizosphere microbial consortia for protection against fungal root pathogens. However, identifying and reconstructing microbial consortia responsible for host protection remains challenging, given the inherent taxonomic and functional complexity of microbiomes. Here, we integrated metagenomic profiling of disease-suppressive microbiomes perturbed by dilution-to-extinction (DTE) with comprehensive culturing and synthetic ecology to identify the key bacterial taxa conferring suppressiveness to the fungal wheat pathogen Fusarium culmorum. Metagenomics of wheat rhizosphere samples along the DTE trajectory revealed bacterial taxa and functions associated with the disease-suppressive phenotype. Crosslinking these DTE metagenome data with a genome-sequenced collection of 336 rhizobacterial isolates from the suppressive soil allowed the reconstruction of synthetic communities (SynComs) of 11 de-replicated strains negatively associated with disease severity. Upon re-introduction in sterilized suppressive soils, this SynCom consistently reproduced the disease-suppressive phenotype. Paired time-series metagenomics and metatranscriptomics of the SynComs pinpointed candidate biosynthetic gene clusters, including a novel non-alpha poly-amino-acid (NAPAA) gene cluster from Arthrobacter, upregulated in presence of F. culmorum. Chemically synthesized NAPAA variants {varepsilon}-poly-L-lysine and {delta}-poly-L-ornithine significantly inhibited F. culmorum hyphal growth. Collectively, our work establishes a transformative strategy for reconstructing microbial consortia that recapitulates beneficial microbiome-associated phenotypes in plant and animal kingdoms.

microbiology↗

bioRxiv2025

Antifungal biosynthesis by root-associated Streptomyces and Pseudomonas is elicited upon plant colonization

Plants are colonized by a diverse microbiome, with microorganisms residing inside and outside of plant tissues. Plants can harness the protective traits of their microbial inhabitants to ward off insect pests and fungal pathogens. However, current understanding of the role of commensal interactions on activating the desired microbial genomic traits remains limited. Here we show that biosynthesis of the antifungal 2,5-dihydro-L-phenylalanine (DHP) by the endophytic Streptomyces sp. PG2 is strongly induced upon colonization of Arabidopsis thaliana. DHP production protects the plant from infection by the fungal root pathogen Rhizoctonia solani, both in vitro and in vivo.. We identified the DHP biosynthetic gene cluster (BGC) and showed that heterologous expression of the BGC in the DHP non-producer Streptomyces coelicolor also conferred plant-inducible DHP production. The BGC was also found in plant-associated Gram-negative bacteria, and in Pseudomonas syringae FF5 we again observed strongly enhanced DHP production upon plant colonization. An ecology-inspired elicitor screen showed that L-valine and brassinosteroid hormones elicit DHP biosynthesis in the plant-beneficial Streptomyces sp. PG2, while L-valine also elicited DHP biosynthesis in S. coelicolor. In vivo experiments confirmed the stimulation of antifungal activity in Streptomyces sp. PG2 by L-valine, while brassinolide mutant plants showed reduced DHP induction. Conversely, neither L-valine nor brassinolide elicited the expression of the DHP BGC in the pathogenic P. syringae, revealing important divergence in the responses to plant signaling, which may reflect selectivity in how endosymbionts and pathogens respond to host cues. Collectively, our data demonstrate that plant colonization can elicit the biosynthetic potential of root-associated microbes, thereby enhancing plant resilience.

microbiology↗

bioRxiv2025

Serotonin modulation of metabolism and stress response in Pseudomonas fluorescens

BackgroundPseudomonas fluorescens is a gram-negative bacterium with a remarkable metabolic and physiological versatility that enables it to adapt and colonize diverse ecological niches, including the human small intestine. While serotonin is primarily found in high concentrations in gut tissue, its levels in the lumen can be elevated in conditions such as celiac disease, where P. fluorescens is also found in increased abundance. The potential effects of serotonin on P. fluorescens in such contexts remain unclear. ResultsWe demonstrate that P. fluorescens metabolizes serotonin primarily into 5-hydroxyindole-3-acetic acid (5-HIAA) and, to a lesser extent, into 5-hydroxytryptophol and N-acetylserotonin. Gene expression analysis revealed significant changes in oxidative stress-related pathways over time, and proteomic analysis confirmed the shifts seen particularly in amino acid catabolic pathways. Serotonin metabolism also enhanced bacterial resistance to oxidative stress, suggesting a protective role. ConclusionsThe findings reveal a novel mechanism by which serotonin modulates the metabolism and stress responses of P. fluorescens. This study provides insight into how P. fluorescens adapts to serotonin-rich environments, such as in celiac disease, and may inform future research on microbial interactions with host-derived metabolites in disease contexts.

microbiology↗

bioRxiv2024

A new pathway in central metabolism mediates nutrient control of development and antibiotic production by Streptomyces

The amino sugar N-acetylglucosamine (GlcNAc) plays a central role in primary metabolism and is a key signaling molecule for the onset of morphological and chemical differentiation of Streptomyces. The global nutrient-sensory regulator DasR acts as the gatekeeper of development in streptomycetes, and its activity is modulated by aminosugar phosphates. Here, we report the discovery of a novel pathway in aminosugar metabolism that governs GlcNAc sensing. GlcNAc-6P is converted into a toxic metabolite via two new enzyme functions, namely dehydration of N-acetylglucosamine-6-phosphate by NagS to form 6P-Chromogen I, a reaction that has not yet been described in the textbooks, and its subsequent deacetylation by NagA producing a cytotoxic structural analogue of ribose. The latter reveals an unexpected promiscuous activity for GlcNAc-6P deacetylase NagA. The crystal structures of NagS apoenzyme and NagS in complex with its substrate GlcNAc-6P or its inhibitor 6-phosphogluconate were resolved at 2.3 [A], 2.6 [A], and 1.7 [A] resolution, respectively. Detailed in vivo and in vitro studies resolved the key residues of the NagS catalytic site. Thus, we have uncovered a novel pathway in aminosugar metabolism that sheds new light on nutrient-mediated control of development and antibiotic production in Streptomyces.

microbiology↗

bioRxiv2024

Prediction of gene cluster function based on transcriptional regulatory networks uncovers a novel locus required for desferrioxamine B biosynthesis

Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining revealed millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, and the major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Studying the regulon of iron master regulator DmdR1 in Streptomyces coelicolor combined with co-expression data and large-scale comparative genome analysis identified the novel desJGH gene cluster. Mutational and metabolomics analysis showed that desJGH is required for biosynthesis of the clinical drug desferrioxamine B. DesJGH thereby dictate the balance between the structurally distinct desferrioxamines B and E. We propose regulation-based genome mining as a promising approach to functionally prioritize BGCs to accelerate the discovery of novel bioactive molecules.

genomics↗

bioRxiv2023

Probiotics supplementation to adult human small intestinal stoma microbiota causes dynamic increase in the community resistance to perturbations and nutrient utilization

The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, dynamic molecular mechanisms are often not elucidated, especially when targeting the small intestinal microbiota. Here, we show that supplementation of a probiotic formula (Ecologic(R)825) to the adult human small intestinal ileostoma microbiota counteracts the growth of Enterococcaceae and Enterobacteriaceae and reduces ethanol production, leading to major changes in nutrient utilization and resistance to perturbations. The observed alterations coincided with an initial increase in lactate production and decrease in pH by the probiotics, followed by a sharp increase in the levels of butyrate and propionate. Additionally, increased production of multiple N-acyl amino acids was detected in the stoma samples supplemented with the probiotic formula. Overall, this study shows how network theory can be used to improve the current or identify novel microbiota-targeted therapies. The outcome may help further understand the reported effects of these probiotic formula on the host.

microbiology↗

bioRxiv2022

The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes

Actinobacteria are prevalent in the rhizosphere and phyllosphere of diverse plant species where they help to enhance tolerance of plants against biotic and abiotic stresses. Here, we show that the plant hormones jasmonic acid (JA) and methyljasmonate (MeJA) alter growth, development and specialized metabolism of Streptomyces. Challenge of Streptomyces coelicolor with JA or MeJA led to strongly enhanced production of the polyketide antibiotic actinorhodin. JA is toxic to Streptomycetaceae, whereby members of the genus Streptacidiphilus are generally more sensitive than streptomycetes. As a defensive response, extensive amino acid conjugation of JA was observed; the most prevalent conjugation was with glutamine (Gln), while conjugates with Val, Tyr, Phe and Leu/Ile were identified after longer exposure to JA. Synthetic JA conjugates failed to activate antibiotic production and had strongly reduced toxicity, strongly suggesting that conjugation inactivates JA and serves to detoxify the hormone. Thus, for the first time we provide evidence that plant hormones modulate growth, development and secondary metabolism of streptomycetes, whereby amino acid conjugation serves as a defense strategy by the bacteria to circumvent plant hormone toxicity. IMPORTANCEMicroorganisms that live on or inside plants greatly influence plant health. Streptomycetes are considered to have an important role in defense against plant diseases, but the mechanisms through which they protect plants are currently not fully understood. It has been suggested that streptomycetes respond to changes in the plants physiology, among others by producing protective molecules; however, little is known of the signal transduction from plant to bacterium. We here demonstrate that the plant hormones jasmonic acid (JA) and methyljasmonate (MeJA) directly influence the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. Jasmonic acid is then modified in the cell by amino acid conjugation, which reduces the bioactivity of the hormone and thus quenches the signal. To the best of our knowledge, this has not been reported previously. Collectively, these results suggest a relationship between plant physiological changes and the response of streptomycetes in multiple ways.

microbiology↗

bioRxiv2022

Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

Ancient microbial communities of permafrost soils and frozen animal remains represent an archive that has barely been explored. This yet unexplored microbial world is a vast resource that can provide us with new evolutionary insights, metabolic pathways and novel chemistry. Here, we reveal that Actinobacteria isolated from a faecal sample from the intestinal tract of a 28,000-year-old Siberian mammoth are phylogenetically and metabolically distinct from currently known modern siblings. Ancient Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of the ancestors show a large phylogenetic distance to strains isolated today and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides a snapshot into Actinobacteria of the past, yielding unexplored genomic information that is not yet present in current databases.

microbiology↗

bioRxiv2021

New from old: discovery of the novel antibiotic actinomycin L in Streptomyces sp. MBT27

Streptomycetes are major producers of bioactive natural products, including the majority of the antibiotics. While much if the low-hanging fruit has been discovered, it is predited that less than 5% of the chemical space has been mined. Here, we describe the novel actinomycins L1 and L2, which are produced by Streptomyces sp. MBT27. The molecules were discovered via metabolic analysis combined with molecular networking of cultures grown with different combinations of carbon sources. Actinomycins L1 and L2 are diastereoisomers, and the structure of actinomycin L2 was resolved using NMR and single crystal X-ray crystallography. Actinomycin L is formed via a unique spirolinkage of anthranilamide to the 4-oxoproline moiety of actinomycin X2, prior to the condensation of the actinomycin halves. Feeding anthranilamide to cultures of Streptomyces antibioticus, which has the same biosynthetic gene cluster as Streptomyces sp. MBT27 but only produces actinomycin X2, resulted in the production of actinomycin L. This shows that actinomycin L results from joining two distinct metabolic pathways, namely those for actinomycin X2 and for anthranilamide. Actinomycins L1 and L2 showed significant antimicrobial activity against Gram- positive bacteria. Our work shows how new molecules can still be identified even in the oldest of natural product families. IMPORTANCEActinomycin was the first antibiotic discovered in an actinobacterium by Selman Waksman and colleagues, as early as 1940. This period essentially marks the start of the golden era of antibiotic discovery. Over time, emerging antimicrobial resistance (AMR) and the declining success rate of antibiotic discovery resulted in the current antibiotic crisis. We surprisingly discovered that under some growth conditions, Streptomyces sp. MBT27 can produce actinomycins that are significantly different from those that have been published so far. The impact of this work is not only that we have discovered a novel molecule with very interesting chemical modifications in one of the oldest antibiotics ever described, but also that this requires the combined action of primary and secondary metabolic pathways, namely the biosynthesis of anthranilamide and of actinomycin X2, respectively. The implication of the discovery is that even the most well-studied families of natural products may still have surprises in store for us.

microbiology↗

bioRxiv2020

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products

Most clinical drugs are based on microbial natural products, with compound classes including polyketides (PKS), non-ribosomal peptides (NRPS), fluoroquinones and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295 Streptomyces genomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a novel subfamily of lanthipeptides, designated Class V. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria. Code and data availabilityThe source code of DecRiPPter is freely available online at https://github.com/Alexamk/decRiPPter. Results of the data analysis are available online at http://www.bioinformatics.nl/~medem005/decRiPPter_strict/index.html and http://www.bioinformatics.nl/~medem005/decRiPPter_mild/index.html (for the strict and mild filters, respectively). All training data and code used to generate these, as well as outputs of the data analyses, are available on Zenodo at doi:10.5281/zenodo.3834818.

microbiology↗