Tuesday, February 18, 2020

A new tier 2 PGDB for Pseudomonas putida KT2440

We are pleased to announce that we have recently upgraded our Pseudomonas putida KT2440 database to a tier 2 status, meaning it has undergone moderate curation. The KT2440 strain is a plasmid-free derivative of the toluene-degrading organism Pseudomonas putida mt-2, which was originally isolated in 1963 under the name Pseudomonas arvilla mt-2. Unlike strain mt-2, strain KT2440 does not carry the pWW0 TOL plasmid, which is required for toluene degradation. Strain KT2440 is the first Gram-negative soil bacterium to be certified as a safety strain by the Recombinant DNA Advisory Committee and is considered the best characterized saprophytic Pseudomonad that has retained its ability to survive and function in the environment. It is used worldwide as a workhorse for genetic and physiological studies and for the development of biotechnological applications.

This upgrade included the following curation activities:

  • Propagation of cumulative changes in MetaCyc compounds and reactions since the KT2440 PGDB was created, synchronizing the two databases. 
  • Rerun of the pathway prediction algorithm, followed by human inspection and pruning of some of the predicted pathways. The pathway count grew by 25, for a total of 330. The number of enzymatic reactions grew from 2,081 to 2,313.
  • Creation of a large number of protein complexes, increasing the total number of complexes from 37 to 180.
  • Propagation of strain KT2440 enzymes that were previously curated in MetaCyc into this PGDB.
  • Curation of several new pathways that were previously not present in MetaCyc.
  • Literature-based curation of 65 proteins.
  • Literature-based curation of 247 transcriptional regulatory interactions.

Some of the newly curated pathways that may be of particular interest:

  • Carbon metabolism in this organism is unusual. Pseudomonas putida KT2440 lacks a functional Embden-Meyerhof-Parnas (EMP) pathway, and 90% of consumed sugar is converted into D-gluconate, entering central carbon metabolism as D-gluconate 6-phosphate, which is processed in two parallel channels: it is either converted to pyruvate via the Entner-Doudoroff shunt, or processed by enzymes of the pentose phosphate pathway into D-glyceraldehyde 3-phosphate. This complex process is described by the pathway “glucose metabolism (Pseudomonas putida)”.
  • The fluorescence of Fluorescent Pseudomonads is due to the production of pyoverdine siderophores. Pyoverdines are species-specific, with more than 100 types reported. A new pathway describes the biosynthesis of pyoverdine G4R, the type produced by this organism.
  • Similarly, there is a wide variability in the composition of Lipid A, a major component of bacterial lipopolysaccharides. Three new pathways describe the biosynthesis of P. putida-specific (Kdo)2-lipid A.

Access to tier 2 PGDBs requires a subscription to the BioCyc website.