The following links provide access to the release notes provided for previous versions of the PMN-generated metabolic pathway databases. Current release notes are also available

• PlantCyc 5.0
• AraCyc 8.0
• PoplarCyc 3.0

• PlantCyc 4.0
• AraCyc 7.0
• PoplarCyc 2.0

• PlantCyc 3.0
• AraCyc 6.0
• PoplarCyc 1.0

• PlantCyc 2.0
• AraCyc 5.0

• PlantCyc 1.0
• AraCyc 4.5

• AraCyc archives
  

PMN Release Notes Archives

The April 2011 release includes updates to all three PMN databases: PlantCyc, AraCyc, and PoplarCyc. PMN and MetaCyc curators, along with contributors from the research community, have added over 40 new pathways and 150 new enzymes to these resources. In addition, the newly updated Pathway Tools software (v.15.0) has some improved capabilities.

We hope that these enhanced resources will be useful to researchers, educators, and students who want to learn more about plant metabolism!

Noteworthy new manually curated pathways:

• Two new pathways ( sciadonic acid biosynthesis and dicranin biosynthesis) describe the production of unusual fatty acids


• The flavor of wine can be affected by tartaric acid biosynthesis.


• Several species of plants produce the insect juvenile hormone III. Researchers are still working to discover how this compound may help plants to defend themselves from insects and /or allow an invasive species to outcompete surrounding plants.


• Several different routes for the biosynthesis of salicylic acid glucosides, such as 2,5-dihydroxybenzoate 2-O-beta-D-glucoside, have been added to give a more comprehensive view of the metabolic fate of this important defense signaling compound.


• Links to recent chapters on plant metabolism from The Arabidopsis Book have been added to many AraCyc pathways.


• Lists of all pathways added to, updated in, or removed from the databases in the most recent releases are available for PlantCyc 5.0, AraCyc 8.0, and PoplarCyc 3.0
.

Major Pathway Tools software upgrade:
A few highlights from the software upgrade from 12.5 to 14.0

• Specialized search interfaces for pathways, compounds, enzymes, and more
• New ability to create and work with groups of items in the desktop version of the software

Noteworthy new manually curated pathways:

• Two new biosynthetic routes (variant IV and variant V) for one of the major cell wall-bound phenolic acids, 4-hydroxybenzoate, have been added to PlantCyc.


• The biosynthetic pathway for serinol, a free amine found on sugarcane leaf surface that has therapeutic potential for the treatment of cancers in the nervous system, can now be seen in PlantCyc.


• The oxidized GTP and dGTP detoxification pathway involved in maintaing genomic integrity by removing mutagenic nucleotides has been entered into PlantCyc, AraCyc, and PoplarCyc


• Two different modes of gibberellin inactivation (methylation and epoxidation) that are present in different species have been added to the appropriate PMN databases.


• Lists of all pathways added to, updated in, or removed from the databases in the most recent releases are available for PlantCyc 4.0, AraCyc 7.0, and PoplarCyc 2.0
.

Overall PMN Highlights

New database:
Using a newly developed PMN enzyme annotation pipeline, the Populus trichocarpa 1.1 genome release sequences provided by JGI, and the Pathologic software from SRI International, the PMN has created the PoplarCyc 1.0 database. Now, researchers focusing on this important tree can see predicted enzymes mapped onto metabolic pathways and can overlay their microarray and metabolomic experimental results onto a poplar metabolic map using the OMICs viewer.

New tool:
Researchers can now do BLAST analyses using nucleotide or protein sequences at the PMN. Two BLAST datasets are available:

• “Reference Enzymes” (14,187 proteins) includes enzymes taken from a number of different data repositories that have experimentally supported* enzyme activity and known protein sequences. Both plant and non-plant enzymes are contained in this data set.


• “PlantCyc Enzymes” (6411 proteins) includes the enzymes found in the PlantCyc database that have known protein sequences. Both experimentally and computationally supported enzymes are present in this data set.

New data:

• Many new pathways, enzymes, reactions, and compounds have been added to the suite of PMN databases.


• The new PMN enzyme annotation pipeline was also applied to the Arabidopsis thaliana genome, resulting in many changes to the set of computationally predicted annotations found in AraCyc.

Collaborator Release Notes

You can find more information on the releases provided by our collaborators at MetaCyc, the multi-species, multi-kingdom database, in their Release Notes