DDRprot: a database of DNA damage response-related proteins

The DNA Damage Response (DDR) signalling network is an essential system that protects the genome’s integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used.E.A.-L. was supported by the European Commission grant [FP7-REGPOT-2012-2013-1; A.A. was partially supported by the Spanish Ministry of Science and Innovation grant [PS09/02111].Peer reviewe

Differentially regulated genes under different growth conditions.

<p>(A) Example of a transcriptionally and translationally upregulated gene in LB compared to BHI control. The novel gene XECs170 is highlighted in pink. The transcription of XECs170 is increased 2.7-fold and translation 9.8-fold. (B) Summary of differentially regulated genes in LB compared to BHI control. For all three gene categories, downregulation dominates. (C) Example of a transcriptionally and translationally downregulated gene in BHI COS compared to BHI control. Transcription of XECs197 is 5.5-fold and translation is 129-fold reduced at the stress condition. (D) Summary of differentially regulated genes in BHI COS compared to BHI control. Downregulation at the translational level clearly dominates for all gene categories.</p

Selected results of PredictProtein for the short annotated genes, and the novel genes with and without annotated homologs.

<p>(A) Average secondary structure composition. (B) Number of predicted transmembrane helices. (C) Number of predicted disulfide bonds. (D) Predicted localization of the proteins within the <i>E</i>. <i>coli</i> cell. Percentage values for every gene separately can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184119#pone.0184119.s010" target="_blank">S8 Table</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184119#pone.0184119.s011" target="_blank">S9 Table</a>.</p

Differentially regulated genes under different growth conditions.

<p>(A) Example of a transcriptionally and translationally upregulated gene in LB compared to BHI control. The novel gene XECs170 is highlighted in pink. The transcription of XECs170 is increased 2.7-fold and translation 9.8-fold. (B) Summary of differentially regulated genes in LB compared to BHI control. For all three gene categories, downregulation dominates. (C) Example of a transcriptionally and translationally downregulated gene in BHI COS compared to BHI control. Transcription of XECs197 is 5.5-fold and translation is 129-fold reduced at the stress condition. (D) Summary of differentially regulated genes in BHI COS compared to BHI control. Downregulation at the translational level clearly dominates for all gene categories.</p

Three novel genes with RIBOseq signals as examples.

<p>In the lower part, the corresponding section of the genome is shown with the novel gene highlighted in pink. In the upper part, the strand-specifically mapped RIBOseq reads are displayed, whereby each black line represents a sequenced read.</p

Conservation of novel genes with and without annotated homologs.

<p>Average AA sequence similarity (according to the color scale) for all target sequences from a tblastn search of the RefSeq genomic database, for each ORF is shown. Each dot represents a hit in the database for a given novel gene, with points combined and similarity averaged by genus. Novel genes are spread across the X-axis ordered by their length; the Y-axis shows the taxonomic distance of each genus, using the SILVA database 16S rRNA alignment guide tree. (A) Novel genes with at least one annotated homologous protein sequence. (B) Novel genes without annotated homologs. Those with annotated homologs tend to be found across more genera. Note that the number of homologs found in each genus is not indicated, with the vast majority being in <i>Escherichia</i> and <i>Shigella</i>. Data overview is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184119#pone.0184119.s007" target="_blank">S5 Table</a>.</p

Growth conditions where the novel genes reach or exceed translation thresholds.

<p>The Venn-Diagram shows how many ORFs are translated under the three growth conditions investigated. The majority of novel genes are translated at optimal growth conditions leading to a large overlap between LB and BHI control. Blue: LB at 37°C, green: BHI at 37°C, red: BHI + 4% NaCl at 14°C.</p

Distribution of 465 small novel genes within the EHEC genome.

<p>The circles from outside to inside show: annotated genes on the plus strand, annotated genes on the minus strand, novel genes on the plus strand and novel genes on minus strand. Novel genes with annotated homologs are colored in blue and novel genes without annotated homologs are colored in orange.</p