title: The Listeria monocytogenes strain 10403S BioCyc database.
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.
authors.affiliation: Department of Food Science, Cornell University, Ithaca, NY 14853, USA rho2@cornell.edu.
authors.forename: Renato H
authors.initials: RH
authors.lastname: Orsi
authors.affiliation: Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Bergholz
authors.affiliation: Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Wiedmann
authors.affiliation: Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Kathryn J
authors.initials: KJ
authors.lastname: Boor
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D006801:Humans; D008089:Listeria monocytogenes / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins
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