diff --git a/README.md b/README.md index ec0b5ae10cd4c288adc3d65ccaa65d4806144e24..29ca7d1e0b777f9a40bcc6134a8c9c18252ee0c1 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,57 @@ Krüger, A., Frunzke, J., & Weber, U. (2025). Genome-wide analysis of DtxR and H [](https://doi.org/10.60534/14s2v-ztq25) -## SFB 1535 MibiNet- Microbial networking – from organelles to cross-kingdom communities -This ARC is part of the [MibiNet project B01](https://www.sfb1535.hhu.de/projects/research-area-b/b01) + +# Table of Contents +1. Abstract +2. Studies +3. Assays +4. Graphical Overview +5. MibiNet + +## 1. Abstract + +The trace element iron is essential for life, but elevated levels can rapidly cause cellular damage through oxidative stress. Bacteria, like *Corynebacterium glutamicum*, tightly regulate iron and heme homeostasis via the global regulators DtxR and HrrA. This study provides the first analysis of the genome-wide binding patterns of these two regulators demonstrating significant differences in binding dependent on the tested iron regimes. +Overall, we identified 25 new DtxR targets and 210 previously unknown HrrA targets, including genes with crucial roles in central metabolism and DNA repair. Notably, DtxR was shown to link iron metabolism to methionine synthesis, which might be important to protect the cell from oxidative stress. Our findings highlight the interconnected nature of DtxR and HrrA networks and underscore the value of condition-specific analysis to deepen the understanding of how bacteria adapt to environmental changes. + +## 2. Studies + +This ARC contains three different studies, each detailing specific aspects of sample preparation. + +[1_TagIntegration](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/studies/1_TagIntegration?ref_type=heads]): Information on plasmid generation sequences used for tag integration. + + +[2_ChAP-Seq](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/studies/2_ChAP-Seq?ref_type=heads): Details on cultivation and pucification conditions for chAP-Seq samples. + +[3_ReporterStrainGeneration](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/studies/3_ReporterStrainGeneration?ref_type=heads): Cloning procedure and strain generation for reporter strains. + +Detailed metadata description can be found in the corresponding `isa.study` files. + + +## 3. Assays + +The [Assays](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/assays?ref_type=heads) folder contains results from individual experiments. Raw and processed data are stored in the `dataset` folder of each assay, while the corresponding protocols are in the `protocol` folder. + +[1-1_GrowthMonitoring-taggedVariants](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/assays/1-1_GrowthMonitoring-taggedVariants?ref_type=heads): Growth monitoring data collected via BioLector. + +[1-2_qPCR-taggedVariants](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/assays/1-2_qPCR-taggedVariants?ref_type=heads): qPCR experiment data and protocols. + +[2-1_Sequencing and Analysis](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/assays/2-1_Sequencing%20and%20Analysis?ref_type=heads): Sequencing data. + +[2-2_ChAP-analysis](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/assays/2-2_ChAP-analysis?ref_type=heads): Data analysis results form sequences generated in Assay 2-1 . + +[3_ReporterAssays](https://git.nfdi4plants.org/sfb1535_mibinet/2025_IronAndHemeRegulatoryNetworks/-/tree/main/assays/3_ReporterAssays?ref_type=heads): BioLector data of the reporter strains. + +Detailed metadata description can be found in the corresponding `isa.assay` files. + + +## 4. Graphical overview +An overview about all processes are displayed in this graph: + + + + + +## 5. SFB 1535 MibiNet- Microbial networking – from organelles to cross-kingdom communities +This ARC is part of the [MibiNet project B01](https://www.sfb1535.hhu.de/projects/research-area-b/b01)