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. 2015 Mar 28;2015:bav027.
doi: 10.1093/database/bav027. Print 2015.

The Listeria Monocytogenes Strain 10403S BioCyc Database

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Free PMC article

The Listeria Monocytogenes Strain 10403S BioCyc Database

Renato H Orsi et al. Database (Oxford). .
Free PMC article

Abstract

Listeria monocytogenes is a food-borne pathogen of humans and other animals. The striking ability to survive several stresses usually used for food preservation makes L. monocytogenes one of the biggest concerns to the food industry, while the high mortality of listeriosis in specific groups of humans makes it a great concern for public health. Previous studies have shown that a regulatory network involving alternative sigma (σ) factors and transcription factors is pivotal to stress survival. However, few studies have evaluated at the metabolic networks controlled by these regulatory mechanisms. The L. monocytogenes BioCyc database uses the strain 10403S as a model. Computer-generated initial annotation for all genes also allowed for identification, annotation and display of predicted reactions and pathways carried out by a single cell. Further ongoing manual curation based on published data as well as database mining for selected genes allowed the more refined annotation of functions, which, in turn, allowed for annotation of new pathways and fine-tuning of previously defined pathways to more L. monocytogenes-specific pathways. Using RNA-Seq data, several transcription start sites and promoter regions were mapped to the 10403S genome and annotated within the database. Additionally, the identification of promoter regions and a comprehensive review of available literature allowed the annotation of several regulatory interactions involving σ factors and transcription factors. The L. monocytogenes 10403S BioCyc database is a new resource for researchers studying Listeria and related organisms. It allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database.

Figures

Figure 1.
Figure 1.
Screenshot of the L. monocytogenes 10403S PGDB genome browser tool. Users can run a quick search for gene names, gene locus, protein name, pathways, reactions or compounds, can login to their private account or create one, which allows the creation and utilization of groups to be analyzed within the database and change the database to be viewed (arrow 1). In the example shown here, the virulence gene actA was selected (arrow 2) and is centered and highlighted within the genome browser window (arrow 3). On top of the genome browser window, users can zoom in and out, move upstream (left) or downstream (right) in the chromosome, select a specific coordinate or gene and have a legend explaining the differences across colors and shapes (arrow 4). Contiguous genes with the same color are part of the same transcription unit (i.e. operon). Transcription start sites are shown as arrows upstream the respective transcription units.
Figure 2.
Figure 2.
Screenshot of the genome overview page. All annotated genes and genetic features are shown. Consecutive genes sharing the same color are part of the same transcription unit (i.e. operon) and share a contiguous underline. Chromosome coordinates are shown on the left and right sides of the page. All items are clickable and take the user to the corresponding genetic feature (e.g. gene, tRNA, rRNA) page.
Figure 3.
Figure 3.
Screenshot of the cellular overview page. The graphic represents all reactions, including transport of compounds across the membrane, predicted to be carried out by the cell. Reactions are represented by blue lines. Different compounds are represented by different geometrical shapes. The compounds are: amino acids (pointing up triangles); carbohydrates (squares); proteins (diamonds); purines (vertical ellipses); pyrimidines (horizontal ellipses); cofactors (pointing down triangles); tRNAs (tee); and other (circles). Transport reactions are shown along the cell membrane (as reddish rectangle). Pathways are shown with background gray shading. Reactions that do not belong to a specific pathway are shown at the right side of the picture with no background gray shading.
Figure 4.
Figure 4.
Screenshots of the regulatory overview page showing different options. The inner ring contains master regulators and σ factors while the outer ring contains genes that are regulated only. Genes that are solely regulated by activators are represented by a plus sign. Genes that are solely regulated by inhibitors are represented by a minus sign. Genes that regulated by both inhibitors and activators are represented by a circle. Genes encoding σ factors are represented by squares. LMRG_02663 encodes the alternative σ factor, σH. (A) Initial page showing the “Operations” menu at the right. (B) Screenshot showing genes directly regulated by σB highlighted in green. Notice that among these genes are the transcription factor encoding genes prfA, mogR, yvoA, hrcA and cggR. C: Screenshot showing genes directly and indirectly regulated by σB. Genes are highlighted with different colors according to the transcription factor that directly regulates them; genes directly regulated by σB are highlighted in green. Genes indirectly regulated by σB and directly regulated by other regulators are color coded in orange (PrfA-regulated genes), light blue (MogR-regulated genes), purple (YvoA-regulated genes), red (CggR-regulated genes) and magenta (HrcA-regulated genes). A list of genes directly regulated by PrfA is shown at the bottom right. (D) Screenshot showing the overlay of experimental data within the regulatory overview. The average fold changes (FC = parent strain/ΔsigB mutant) of significantly σB positively regulated genes identified in an RNA-Seq study by (25) were overlaid. A legend at the top left part of the figure shows the color-coding associated with the amplitude of the FC. A “Omics Data Report Table” providing some summary statistics is also shown at the bottom left part of the screenshot. Notice that most genes identified in that study as being σB-dependent are solely regulated by σB.
Figure 5.
Figure 5.
Screenshot of the gene gadD3 page. The page includes several useful pieces of information such as (1) enzyme name, gene name, gene locus name and synonymous names; (2) a summary diagram of the expression regulation; (3) a summary text with pertinent information associated with the gene or protein, literature citations, genome localization, and protein molecular weight; (4) schematics representing the reactions carried out by the enzyme and the regulatory interactions involved in the gene expression regulation; (5) Gene ontology terms associated with the protein function; (6) MultiFun terms associated with the protein function and credits; (7) information on the reaction(s) carried out by the enzyme, including the pathways (if any) where this reaction may occur; (8) a diagram representing the region where the gene is located in the genome, including neighboring genes, promoters and regulatory regions and the transcription unit(s) associated with the gene; (9) bibliographical references with links to NCBI PubMed and (10) an “Operations” box with several options for comparative genomics analyses using the gene.

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