Seif2019 - Strain-specific metabolic models of Salmonella

  public model
Short description
Seif, 2019 - Systems biology and pangenome of Salmonella O-antigens Strain-specific metabolic models of Salmonella strains updated with O-antigen metabolic pathways. Locus-tags are updated in this version of the models to include both the prokka annotations and the refseq locus tags.
Format
Original code
Related Publication
  • Systems Biology and Pangenome of Salmonella O-Antigens.
  • Yara Seif, Monk JM, Machado H, Kavvas E, Palsson BO
  • mBio , 8/ 2019 , Volume 10 , Issue 4
  • Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
  • O-antigens are glycopolymers in lipopolysaccharides expressed on the cell surface of Gram-negative bacteria. Variability in the O-antigen structure constitutes the basis for the establishment of the serotyping schema. We pursued a two-pronged approach to define the basis for O-antigen structural diversity. First, we developed a bottom-up systems biology approach to O-antigen metabolism by building a reconstruction of Salmonella O-antigen biosynthesis and used it to (i) update 410 existing Salmonella strain-specific metabolic models, (ii) predict a strain's serogroup and its O-antigen glycan synthesis capability (yielding 98% agreement with experimental data), and (iii) extend our workflow to more than 1,400 Gram-negative strains. Second, we used a top-down pangenome analysis to elucidate the genetic basis for intraserogroup O-antigen structural variations. We assembled a database of O-antigen gene islands from over 11,000 sequenced Salmonella strains, revealing (i) that gene duplication, pseudogene formation, gene deletion, and bacteriophage insertion elements occur ubiquitously across serogroups; (ii) novel serotypes in the group O:4 B2 variant, as well as an additional genotype variant for group O:4, and (iii) two novel O-antigen gene islands in understudied subspecies. We thus comprehensively defined the genetic basis for O-antigen diversity.IMPORTANCE Lipopolysaccharides are a major component of the outer membrane in Gram-negative bacteria. They are composed of a conserved lipid structure that is embedded in the outer leaflet of the outer membrane and a polysaccharide known as the O-antigen. O-antigens are highly variable in structure across strains of a species and are crucial to a bacterium's interactions with its environment. They constitute the first line of defense against both the immune system and bacteriophage infections and have been shown to mediate antimicrobial resistance. The significance of our research is in identifying the metabolic and genetic differences within and across O-antigen groups in Salmonella strains. Our effort constitutes a first step toward characterizing the O-antigen metabolic network across Gram-negative organisms and a comprehensive overview of genetic variations in Salmonella.
Contributors
Krishna Kumar Tiwari, Yara Seif

Metadata information


Curation status
Non-curated

Tags
Name Description Size Actions

Model files

Strain_specific_models_sbml.zip Strain-specific genome scale metabolic models of Salmonella updated with O-antigen biosynthesis pathways 108.86 MB Preview | Download

  • Model originally submitted by : Yara Seif
  • Submitted: 11-Sep-2019 18:06:02
  • Last Modified: 11-Sep-2019 18:06:02
Revisions
  • Version: 6 public model Download this version
    • Submitted on: 11-Sep-2019 18:06:02
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Edited model metadata online.