Data and code relative to the Ricciardelli et al. 2024 manuscript on the effect of trace metals in controlling the metabolic shifts between alternative electron acceptors in Escherichia coli and other oganisms. The E. coli genome is available in NCBI under project PRJNA1129478, while the proteomic data are available in the PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) at the European Bioinformatics Institute (EMBL-EBI, Hinxton, Cambridge, UK) with accession number XXXXXXXXX.
This repository contains the following files:
- README.md (this readme file)
- GEM-collection_MAGs_annotation.ipynb containing the code for the plotting of the MAGs terminal reductase data
- hmm_moldes folder, containing the hmm profiles used to annotate the MAGs downloaded from the JGI GEM collection.
- hmm_moldes folder, containing the individual results from the hmmer3 search obtained using the follwing command:
hmmsearch --cpu 12 --tblout results_table_gene.txt MODEL.hmm.gz GEM_combined_mags.faa.gz > results_gene.log - Ecoli_k12_DH5.fna containing the nucleotide fasta file of the E. coli genome
- Ecoli_k12_DH5.gff containign the gff annotation of the E. coli genome
- Ecoli_growth_data.csv containing the growth experiment data for E. coli
- Bsubtili_growth_data.csv containing the growth experiment data for Bacillus subtilis
- Sbacillaris_growth_data.csv containing the growth experiment data for Stichococcus bacillaris
- Sbacillaris_rETR_data.csv containiong the rETR data from S. bacillaris
- IPCMS_metal_data.csv containing the results of the ICP-MS trace metal data
- DE_proteins_proteome folder, contaning the tables of the differentially expressed genes at the 3 time points
Please cite as:
Annarita Ricciardelli, Benoit de Pins, Jacopo Brusca, Monica Correggia, Luciano Di Iorio, Martina Cascone, Marco Giardina, Stefany Castaldi, Rachele Isticato, Roberta Iacono, Marco Moracci, Nunzia Nappi, Antonino Pollio, Costantino Vetriani, Serena Leone, Angelina Cordone, Donato Giovannelli1. 2024. Trace elements availability controls terminal electron acceptor utilization in Escherichia coli. BioArXiv