PRODORIC: state-of-the-art database of prokaryotic gene regulation

Abstract

PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.

Figure 1.

Number of transcription factors per organism compared to the 2017 release of PRODORIC. Gray bars are the transcription factors in the previous version of PRODORIC. Red and orange hatched boxes are the transcription factors removed from PRODORIC or merged with other datasets, respectively. Green bars are new transcription factors added in this release. Numbers above the bars are the increase in percent compared to the 2017 release minus removed or merged datasets.

Figure 2.

Additional regulatory data for 1875 different operons. Multiple binding sites per operon have been omitted. (A) Regulatory mode of action for operons. (B) Transcription factor binding regulation.

Figure 3.

Venn diagram showing the number of binding sites elucidated by experiments categorized into three groups of experimental evidence. Sigma factors are not categorized into the three groups of experimental evidence.

Figure 4.

Matrix summary page of the transcription factor TnrA of B. subtilis (MX000026). (A) Desktop view with binding site table. (B) Mobile view with binding sites in tile view.

Figure 5.

Experimental evidence indicator used on the PRODORIC website. The three segments represent the three evidence groups. Independently from the evidence group, segments can have three colors, red (one evidence group covered), yellow (two groups covered) and green (all three groups covered).

Figure 6.

Network visualization example of the transcription factor CsrR from Streptococcus pyogenes (MX000041). The transcription factor (grey ellipse) regulates operons (white square) or genes (rounded box), the regulation type is indicated by arrows: activation (green), repression (red). The expression of the transcription factor is indicated by the dashed grey arrow. The color of the genes indicates members of the same operon.