EcoCyc: a comprehensive view of Escherichia coli biology

Abstract

EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E. coli. Recent EcoCyc developments include a new initiative to represent and curate all types of E. coli regulatory processes such as attenuation and regulation by small RNAs. EcoCyc has started to curate Gene Ontology (GO) terms for E. coli and has made a dataset of E. coli GO terms available through the GO Web site. The curation and visualization of electron transfer processes has been significantly improved. Other software and Web site enhancements include the addition of tracks to the EcoCyc genome browser, in particular a type of track designed for the display of ChIP-chip datasets, and the development of a comparative genome browser. A new Genome Omics Viewer enables users to paint omics datasets onto the full E. coli genome for analysis. A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc.

Figure 1.

Graphical representation of the electron transfer reaction catalyzed by NADH:ubiquinone oxidoreductase I (NDH-1). The cellular location of the reaction substrates, electron flow from the cytoplasmic substrates to the membrane-localized ubiquinone and vectorial proton transport across the membrane are shown. A summary reaction equation corresponding to the Enzyme Commission nomenclature (which does not include proton and electron flow) is shown below the graphical representation.

Figure 2.

Graphical representation of the electron transfer pathway between the NDH-1 and cytochrome bo terminal oxidase enzyme complexes. The pathway couples the oxidation of NADH to the reduction of oxygen to water via transfer of electrons in the membrane by ubiquinone/ubiquinol and includes proton transport across the membrane by both enzymes, which generates a proton-motive force.

Figure 3.

Graphical representation of regulation of the thrLABC operon by transcriptional attenuation. When the charged tRNAs L-isoleucyl-tRNA^Ile or L-threonyl-tRNA^Thr are available in the cell, the thrL open reading frame is translated freely, leading to the formation of the attenuator secondary structure (represented by a lollipop icon) and termination of transcription by RNA polymerase. The negative effect on transcription is indicated by red color of the icons for the charged tRNAs, and the termination of transcription is indicated by X at the location of the attenuator.

Figure 4.

Graphical representation of the regulation of glmUS expression by the transcription factor NagC and the small RNA GlmZ. Transcription initiation at the glmUS promoter is positively regulated by NagC, and is represented by green boxes at the NagC binding sites. The small RNA GlmZ positively regulates translation of the glmS open reading frame via base-pairing, which is indicated by short lines connecting GlmZ with the mRNA.

Figure 5.

The track capabilities of the genome browser. Three tracks are shown below the depicted genes and promoters. The first (highest) of the three tracks is a graph track that is designed to depict ChIP-chip datasets. Graph tracks plot positional information against the genome, and include a Y-component that depicts an intensity value associated with a genome region. Each point in the graph track depicts a ChIP-chip measurement at a given genome region. Its intensity is shown both in the height dimension and in the selected color. Below the graph track are two horizontal tracks that depict the same ChIP-chip dataset, but without the height information–intensities are depicted with color only. Two horizontal tracks are shown to eliminate visual overlap between the regions.

Figure 6.

The multi-genome browser displays a gene and its orthologs across multiple organisms. Hash marks show the starting gene of interest. Orthologs—including, but not limited to, the starting gene—are marked by colors.

Figure 7.

The Genome Omics Viewer enables the analysis of large-scale data sets in the context of the entire E. coli genome. Colors show gene expression based on user-defined benchmarks. Membership in transcription units is indicated by the lines below the genes. Users can click through from individual genes to the appropriate gene page within EcoCyc.