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44 results for “siderophore”
Data and code from: SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration
<h1>TMAP of COCONUT database</h1> <p>The script and data used in SIDERITE paper to generate TMAP picture (Figure S3 in supplementart material).</p> <p>Requirement: tmap</p> <p>You can install tmap by conda.</p> <blockquote> <p>conda create -n tmap python=3.7</p> <p>conda activate tmap</p> <p>conda install -c tmap tmap</p> <p>pip install faerun</p> <p>pip install matplotlib</p> <p>conda install scipy</p> <p>conda install -c rdkit rdkit</p> <p>conda install -c conda-forge mhfp</p> </blockquote> <p> </p> <p>Usage: python plot_COCONUT.py</p> <p>Then it will use COCONUT.csv to generate index.html and index.js. Open index.html to see result.</p> <h1>Other large input files</h1> <p>Tanimoto_COCONUT_SIDERITE.xlsx is the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/predicted_new/Clustering_coconut.m">SIDERITE/predicted_new/Clustering_coconut.m at main · RuolinHe/SIDERITE</a>.</p> <p> </p> <p>Sid_structure_output3.xlsx is used in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/statistics/Figure1.m" target="_blank" rel="noopener">SIDERITE/statistics/Figure1.m at main · RuolinHe/SIDERITE</a>, <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/tmap_code.m" target="_blank" rel="noopener">SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE</a> and <a href="https://github.com/RuolinHe/SIDERITE/blob/main/siderophore_process/Sid_process_code.m" target="_blank" rel="noopener">SIDERITE/siderophore_process/Sid_process_code.m at main · RuolinHe/SIDERITE</a>.</p> <p> </p> <p>COCONUT4MetFrag_Canonical.xlsx is the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/tmap_code.m" target="_blank" rel="noopener">SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE</a>.</p> <p> </p> <p>COCONUT_r.txt is the output file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/tmap_code.m" target="_blank" rel="noopener">SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE</a>. and the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/predicted_new/isSiderophore1.py" target="_blank" rel="noopener">SIDERITE/predicted_new/isSiderophore1.py at main · RuolinHe/SIDERITE.</a></p> <p> </p> <p>COCONUT4MetFrag.xlsx is the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/CheckSMILES2.py" target="_blank" rel="noopener">SIDERITE/TAMP/CheckSMILES2.py at main · RuolinHe/SIDERITE</a>.</p> <p> </p>
Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad
<p>Microbial invasions can compromise ecosystem services and spur dysbiosis and disease in hosts. Nevertheless, the mechanisms determining invasion outcomes often remain unclear. Here, we examine the role of iron-scavenging siderophores in driving invasions of <em>Pseudomonas aeruginosa</em> into resident communities of environmental pseudomonads. Siderophores can be "public goods" by delivering iron to individuals possessing matching receptors; but they can also be "public bads" by withholding iron from competitors lacking these receptors. Accordingly, siderophores should either promote or impede invasion, depending on their effects on invader and resident growth. Using supernatant feeding and invasion assays, we show that invasion success indeed increased when the invader could use its siderophores to inhibit (public bad) rather than stimulate (public good) resident growth. Conversely, invasion success decreased the more the invader was inhibited by the residents' siderophores. Our findings identify siderophores as a major driver of invasion dynamics in bacterial communities under iron-limited conditions.</p>
Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad
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Station ALOHA seasonal siderophore concentrations and iron uptake
<p>Seasonal total siderophore concentrations and surface (15 m) and 300 m iron uptake from Station ALOHA.</p>
FhuF, a ferric-siderophore reductase from E. coli K-12 - X-ray diffraction raw data set
<p>This diffraction data set was collected at 100 K to 1.9 Å resolution at ALBA Synchrotron Beamline XALOC on December 5, 2021.</p>
Data from: Local adaptation, geographical distance and phylogenetic relatedness: assessing the drivers of siderophore-mediated social interactions in natural bacterial communities
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Data from: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways
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Siderophore synthetase-receptor gene coevolution reveals habitat and pathogen-specific bacterial iron interaction networks
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Data from: Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination
Some microbial public goods can provide both individual and community-wide benefits, and are open to exploitation by non-producing species. One such example is the production of metal-detoxifying siderophores. Here, we investigate whether conflicting selection pressures on siderophore production by heavy metals – a detoxifying effect of siderophores, and exploitation of this detoxifying effect – results in a net increase or decrease. We show that the proportion of siderophore-producing taxa increases along a natural heavy metal gradient. A causal link between metal contamination and siderophore production was subsequently demonstrated in a microcosm experiment in compost, in which we observed changes in community composition towards taxa that produce relatively more siderophores following copper contamination. We confirmed the selective benefit of siderophores by showing that taxa producing large amount of siderophores suffered less growth inhibition in toxic copper. Our results suggest that ecological selection will favour siderophore-mediated decontamination, with important consequences for potential remediation strategies.
Data from: Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia.
Abstract. Explaining how cooperation can persist in the presence of cheaters, exploiting the cooperative acts, is a challenge for evolutionary biology. Microbial systems have proved extremely useful to test evolutionary theory and identify mechanisms maintaining cooperation. One of the most widely studied system is the secretion and sharing of iron-scavenging siderophores by Pseudomonas bacteria, with many insights gained from this system now being considered as hallmarks of bacterial cooperation. Here, we introduce siderophore secretion by the bacterium Burkholderia cenocepacia H111 as a novel parallel study system, and show that this system behaves differently. For ornibactin, the main siderophore of this species, we discovered a novel mechanism of how cheating can be prevented. Particularly, we found that secreted ornibactin cannot be exploited by ornibactin-defective mutants because ornibactin receptor and synthesis genes are co-expressed from the same operon, such that disruptive mutations in synthesis genes compromise receptor availability required for siderophore uptake and cheating. For pyochelin, the secondary siderophore of this species, we found that cheating was possible, but the relative success of cheaters was positive frequency-dependent, thus diametrically opposite to the Pseudomonas and other microbial systems. Altogether, our results highlight that expanding our repertoire of microbial study systems leads to new discoveries and suggest that there is an enormous diversity of social interactions out there in nature, and we might have only looked at the tip of the iceberg so far.
The dataset archives of SIDERITE (siderophore information database)
<p>The update of <a href="https://siderite.bdainformatics.org/">SIDERITE</a>.</p> <p>It covers all 918 known siderophores from 1635 records as of Jan 2025.</p> <p dir="auto"><strong>SIDERITE_records_20250131.xlsx</strong><br>contains 1635 siderophore records</p> <p dir="auto"><strong>SIDERITE_unique_structures_20250131.xlsx</strong><br>contains 918 unique siderophore structures</p> <p>The same siderophore structures can be found in different species, leading to multiple records. Therefore, the number of siderophore records can exceed the number of unique siderophore structures.</p> <p><strong>Non-natural_siderophore_records_20250131.xlsx</strong><br>As SIDERITE is a natural product database, it doesn’t include artificial siderophores, those synthesized by supplementing precursors, or variants produced by gene knock-out strains, though we record their names and references as supplements.</p> <p>If you find SIDERITE useful, please cite:</p> <p>Ruolin He, Shaohua Gu, Jiazheng Xu, et al. 2024. “ SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration.” iMeta e192. <a href="https://doi.org/10.1002/imt2.192">https://doi.org/10.1002/imt2.192</a></p> <div> </div> <div><span><span><span>Ruolin</span> <span>He</span></span>, <span><span>Jiazheng</span> <span>Xu</span></span>, <span><span>Jiqi</span> <span>Shao</span></span>, et al.<span><span> 2025. " Tracing Siderophore Precursors to Primary Metabolism for Ecological Applications. " </span></span></span><span>bioRxiv.</span><span> <a href="https://doi.org/10.1101/2025.04.30.651379">https://doi.org/10.1101/2025.04.30.651379</a></span></div>
The MD simulation results for the paper "Multifaceted regulation of siderophore synthesis by multiple regulatory systems"
<p>"MD results.zip" contains the initial structures and trajectories, while the other file comprises the input files generated by CHARMM-GUI.”</p>
Dissolved Siderophore Concentrations Station ALOHA
<p>Dissolved (< 0.2 um) siderophore concentrations measured at Station ALOHA in different seasons.</p>
Mesopelagic Fe bacteria siderophore data
<p>This dataset includes the siderophore measurements made from the Fe bacteria incubation experiments conducted on Gradients 4 and Gradients 5. The siderophore data represents a pooled sample from each of the three replicates for each treatments in the experiments. The cell abundance numbers are presented as an average of the cell abundance measurements made from triplicate treatments. These average cell abundance values are used to calculate the cell normalized siderophore concentrations (siderophore quota), and the error represented the relative error derived from the cell abundance standard deviation from triplicate treatments.</p>
Fig. 6 in Feature-based molecular networking-guided discovery of siderophores from a marine mesophotic zone Axinellida sponge-associated actinomycete Streptomyces diastaticus NBU2966
Fig. 6. NMR calculation results of 8. (a) Linear correlation plots of computed vs experimental 13C and 1H NMR chemical shifts. (b) Relative errors between the computed NMR values and experimental values. (c) The evaluation of NMR calculation results with statistical parameter MAE and CMAE.
Fig. 5 in Feature-based molecular networking-guided discovery of siderophores from a marine mesophotic zone Axinellida sponge-associated actinomycete Streptomyces diastaticus NBU2966
Fig. 5. NMR calculation results of two plausible isomers of 6. (a) Linear correlation plots of experimental vs computed 13C NMR chemical shifts. (b) Relative errors between the computed 13C NMR values of two potential structures and experimental 13C NMR chemical shifts. (c) The evaluation of calculation results with statistical parameter ME (Maximum Error), CME (Corrected Maximum Error), and CMAE (Corrected Mean Absolute Error).
Fig. 2 in Feature-based molecular networking-guided discovery of siderophores from a marine mesophotic zone Axinellida sponge-associated actinomycete Streptomyces diastaticus NBU2966
Fig. 2. Structures of siderophores 1–10. Three types of iron-chelating moieties are marked with blue, red, and purple, respectively. Previously undescribed natural products are highlighted with red subscript numbers. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Feature-based molecular networking-guided discovery of siderophores from a marine mesophotic zone Axinellida sponge-associated actinomycete Streptomyces diastaticus NBU2966
Fig. 1. Detected chemistries of the EtOAc extract of Streptomyces sp. NBU2966 as generated by LC-MS/MS, which was analyzed using NAP, Dereplicator+, and MolNetEnhancer workflow via the GNPS platform. With this network, wherein nodes represent a precursor ion, and its size is scaled to signal intensity and the thickness of edge between nodes suggests the similarity of fragment pattern. (a) Structural annotation for molecular families, wherein the color of nodes denotes the structural annotation at the superclass level by NAP. (b) Observation of molecular family A allows highlighting dereplicated (R)-2-(2-Hydroxyphenyl)-4-hydroxymethyl-4,5-dihydrothiazole. (c) Observation of molecular family B allowed to highlighting dereplicated pyochelin methyl ester. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Siderophore-profile in Allergic and Non-allergic Subjects
ClinicalTrials.gov study NCT03815981. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Data from: Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination
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