CapsuleFinder is a program that detects capsule systems with high accuracy in proteic sequences. It is based on the use of HMM profiles for the detection of the essential proteins of capsule biogenesis and requires computational models describing the number of components and their genetic organization.
Extracellular capsules, when present, constitute the outermost layer of prokaryotic cells and establish the first contact between the microorganism and its environment. They fullfill a myriad of roles often linked to colonization and persistence. The physical properties of capsules allow microorganisms to prevent dessication by retaining moisture near the cell surface and to protect cells from phagocytosis by grazing protozoa. Capsules also play an essential role during infection; they downregulate pro-inflammatory cytokines, protect cells against reactive oxygen species generated by the host, and help bacteria to evade phagocytosis and complement activation: Capsules also reduce the efficiency of antibiotics and cationic antimicrobial peptides.
Capsules are very diverse genetically can be synthesized through different pathways. Accordingly, we have designed eight different capsule models:
- Group I or Wxz/Wzy-dependent
- Group II and III or ABC-dependent
- PGA capsule (Poly-γ-d-glutamate proteic capsule)
- Synthase-dependent capsules, divided in two subtypes:
- Syn_has or Hyaluronic acid capsules
- Syn_cps3 or capsules of type cps3
- Group IV capsules are subdivided in three subtypes:
- GroupIV_f, based on Francisella tularensis GroupIV capsule
- GroupIV_e, based on Escherichia coli GroupIV capsule
- GroupIV_s, based on Salmonella sp. GroupIV capsule
Authors: Olaya Rendueles and Eduardo Rocha
Reference: Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens. Rendueles O, Garcia-Garcerà M, Néron B, Touchon M, Rocha EPC. PLoS Pathog. 2017 Jul 24;13(7):e1006525. doi: 10.1371/journal.ppat.1006525.