Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 4;46(D1):D320-D326.
doi: 10.1093/nar/gkx1091.

PRODORIC2: the bacterial gene regulation database in 2018

Denitsa Eckweiler  1 , Christian-Alexander Dudek  2 , Juliane Hartlich  1 , David Brötje  1 , Dieter Jahn  1
Affiliations

PRODORIC2: the bacterial gene regulation database in 2018

Denitsa Eckweiler et al. Nucleic Acids Res. .

Abstract

Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool. Moreover, binding sites deduced from high-throughput experiments were included. Data for 6 new bacterial species including bacteria of the Rhodobacteraceae family were added. Finally, a comprehensive collection of sigma- and transcription factor data for the nosocomial pathogen Clostridium difficile is now part of the database. PRODORIC2 is publicly available at http://www.prodoric2.de.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Scheme of the PRODORIC2 database showing 19 of its 20 tables.
Figure 2.
Figure 2.
A matrix report page for the transcription factor FnrL from D. shibae. Links providing additional information about the reference strain and the transcription factor are depicted at the top of the page. The position weight matrix is shown in tabulated form and the corresponding binding sites (here truncated) are shown below the matrix as they appear in the original manuscript. Their genomic coordinates, strand orientation and the original citation(s) are provided as well. The accession numbers of the TFBSs are hyperlinked to the NCBI genome browser.
Figure 3.
Figure 3.
Virtual Footprint output generated with a search using the C. difficile SigG PWM. The number of hits has been shortened. Strain information is available as a hyperlink to NCBI.
See this image and copyright information in PMC

References

    1. Tielen P., Schobert M., Härtig E., Jahn D.. Filloux AAM. Anaerobic regulatory networks in bacteria. Bacterial Regulatory Networks. 2012; Norwich: Horizon Academic Press; 273–305.
    1. Hartig E., Jahn D.. Regulation of the anaerobic metabolism in Bacillus subtilis. Adv. Microb. Physiol. 2012; 61:195–216. - PubMed
    1. Galas D.J., Schmitz A.. DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 1978; 5:3157–3170. - PMC - PubMed
    1. Garner M.M., Revzin A.. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 1981; 9:3047–3060. - PMC - PubMed
    1. Oliphant A.R., Brandl C.J., Struhl K.. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol. Cell. Biol. 1989; 9:2944–2949. - PMC - PubMed

Publication types

Substances

LinkOut - more resources