Volatile Esters & Polyphosphate Reactions

[uliebal]

Main improvements in this PR:

• Addition of in total 36 reactions: 15 enzymatic reactions, 10 transport and 9 exchange reactions.
• Addition of in total 26 metabolites.
• Addition of in total 1 gene.

Volatile esters

• 8 new distinct ester reactions are introduced, of these 6 had the substrates already in the model and only the ester metabolite was newly added.
• The esterases have broad substrate flexibility and the existing gene for the esterase was used (YOR126C)
• For two esters, the acid substrate was not available in the model and a new aldehyde dehydrogenase reaction was added to generate the acid.
• The aldehyde dehydrogenase was used from an existing gene (YOR374W or YPL061W) which is supported by literature.
• The ester reactions were added only to the cytoplasm compartment

Polyphosphate reactions

• A polyphosphate synthesis reaction was added by which cytoplasmic ATP generates diphosphate in the vacuole.
• The protein Vtc4p is responsible for polyphosphate synthesis, but is part of a heterogeneous protein complex. However, only the direct related gen for Vtc4p, YJL012C, and no complex partners (Vtc1-5) were added to the GPR.
• Transport of polyphosphate between the compartments was added, as supported by literature. The transport mode was copied from the phosphate transport as H+ symport.
• Polyphosphate phosphatase was added for compartments vacuole, mitochondria and nucleus according to literature.
• Inorganic phosphate in the nucleus was added as new metabolite.

Developers

• Ulf Liebal: [email protected]
• Lars M. Blank: [email protected]
• Hendrik Mengers: [email protected]

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected develop as a target branch (top left drop-down menu)
• If needed, asked first in the Gitter chat room about this PR

[edkerk]

This PR does not allow commits from maintainers, as the fork is under an organisation account (and then it doesn't work). Therefore, #337 replaces this PR.