Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803

Abstract

Despite being a highly studied model organism, most genes of the cyanobacterium Synechocystis sp. PCC 6803 encode proteins with completely unknown function. To facilitate studies of gene regulation in Synechocystis, we have developed Synergy (http://synergy.plantgenie.org), a web application integrating co-expression networks and regulatory motif analysis. Co-expression networks were inferred from publicly available microarray experiments, while regulatory motifs were identified using a phylogenetic footprinting approach. Automatically discovered motifs were shown to be enriched in the network neighborhoods of regulatory proteins much more often than in the neighborhoods of non-regulatory genes, showing that the data provide a sound starting point for studying gene regulation in Synechocystis. Concordantly, we provide several case studies demonstrating that Synergy can be used to find biologically relevant regulatory mechanisms in Synechocystis. Synergy can be used to interactively perform analyses such as gene/motif search, network visualization and motif/function enrichment. Considering the importance of Synechocystis for photosynthesis and biofuel research, we believe that Synergy will become a valuable resource to the research community.

Figure 1. Overview of the data and methods used in the study.

A co-expression network was inferred from gene expression, and promoter motifs were identified de novo from the genome sequences of orthologous species. The motif information was used to investigate if transcription factor neighborhoods were enriched for motifs compared to random network neighborhoods.

Figure 2. Clustered co-expression network.

A clustered co-expression network derived from the complete co-expression network at a CLR threshold of 4.0. Each node corresponds to a set of clustered genes. The size of the nodes is proportional to the number of genes in the cluster. Two clusters are linked if they share at least one co-expressed gene pair. The annotations correspond to the most significantly enriched GO terms in the clusters (q<0.05).

Figure 3. Central motifs mapped to Synechocystis promoters.

The plots show the total number of times the central motifs were mapped to promoters (A), the number of unique motifs that were mapped (B) and the number of unique genes the motifs were mapped to (C) for different FIMO q-value thresholds.

Figure 4. Gene co-expression neighborhoods with significant motif enrichment.

The figure plots the fraction of neighborhoods for regulatory genes (A) and DNA-binding genes (B) with at least one significantly enriched motif (q<0.05) against the q-value threshold for mapping motifs to the genome. The fractions are calculated from the total number of genes in the respective groups that have gene expression data (118 DNA-binding genes and 136 regulatory genes). Plots are shown for all motifs and the subset of central motifs as well as for the complete and subset co-expression networks with different CLR thresholds. P-values are given for each combination of parameters and indicate the probability of observing the reported fraction of enriched neighborhoods in randomized networks.

Figure 5. Conservation of photosynthesis genes.

Co-expressed genes related to photosynthesis in Synechocystis (A) were BLASTed against A. thaliana. The orthologs (BLAST E-value <1e-5) were compared against P. trichocarpa (B) and O. sativa (C) using the network comparison tool ComPlEx. This revealed conservation of co-expression across all four species. Note that the A. thaliana genes given in white color were not measurably expressed in the other species.

Figure 6. Web application screenshots.

Gene search interface (A), network viewer (B), gene details (C) and motif details (D).

Figure 7. Synergy case study 1.

A regulatory motif and its transcription factor were extracted from the literature . Searching for the motif in Synergy identified a number of genes that were experimentally determined to be regulated by this transcription factor.