CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks

Mariana Teixeira Dornelles Parise,Josch Konstantin Pauling,Vasco Ariston De Carvalho Azevedo,Rodrigo Bentes Kato,Jan Baumbach,Andreas Tauch,Doglas Parise

doi:10.1038/s41597-020-0484-9

Mariana Teixeira Dornelles Parise, Josch Konstantin Pauling + Show 5 more

Open Access

https://doi.org/10.1038/s41597-020-0484-9

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Abstract

We present the newest version of CoryneRegNet, the reference database for corynebacterial regulatory interactions, available at www.exbio.wzw.tum.de/coryneregnet/. The exponential growth of next-generation sequencing data in recent years has allowed a better understanding of bacterial molecular mechanisms. Transcriptional regulation is one of the most important mechanisms for bacterial adaptation and survival. These mechanisms may be understood via an organism’s network of regulatory interactions. Although the Corynebacterium genus is important in medical, veterinary and biotechnological research, little is known concerning the transcriptional regulation of these bacteria. Here, we unravel transcriptional regulatory networks (TRNs) for 224 corynebacterial strains by utilizing genome-scale transfer of TRNs from four model organisms and assigning statistical significance values to all predicted regulations. As a result, the number of corynebacterial strains with TRNs increased twenty times and the back-end and front-end were reimplemented to support new features as well as future database growth. CoryneRegNet 7 is the largest TRN database for the Corynebacterium genus and aids in elucidating transcriptional mechanisms enabling adaptation, survival and infection.

Highlights

Next-generation sequencing (NGS) has unraveled the genomic sequence of a multitude of bacterial genomes[1]
In the seventh version of CoryneRegNet, we present 82,268 regulatory interactions, an increase of more than eleven times compared to the sixth version, as well as 228 transcriptional regulatory networks (TRNs), increasing the number of corynebacterial strains with known TRNs by twenty times
We present an increase of more than seven times the number of corynebacterial species with TRNs available in public databases representing a great improvement for the bacterial gene regulatory network research community

Summary

Introduction

Next-generation sequencing (NGS) has unraveled the genomic sequence of a multitude of bacterial genomes[1]. The main players in the transcriptional regulation of bacterial organisms are transcription factors (TFs) These regulatory proteins recognize transcription factor binding sites (TFBSs) in the upstream region of the respective target genes (TGs), stimulating or repressing their expression[4,5,6]. Experimental studies such as RNA-Seq[7], microarray[8], ChIP-chip and ChIP-seq[9] have been applied in order to reveal regulatory interactions in a cell. These experimental data are not available for every member of a bacterial genus

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