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YeastCyc Update History

YeastCyc Statistics by Year
2021 2019 2017 2016 2015 2014 2013 2012 Description
Pathways 307 312 292 286 270 270 259 154 Number of metabolic and signaling pathways, excluding super-pathways
Reactions 1945 2053 1650 1491 1389 1402 1378 991 Number of biochemical reactions
Polypeptides 5944 6610 5836 5846 5876 5893 5880 837 Number of polypeptides
Protein complexes 741 738 168 165 106 99 91 56 Number of protein complexes
Transporters 224 237 56 48 49 51 51 0 Number of transporters that catalyze transport reactions
Compounds 1261 1573 1240 1208 1047 1046 1020 692 Number of compounds
Citations 47134 14705 14078 2848 2096 1760 1546   Number of citations
 

Release Notes for YeastCyc Version 23.1

Released on Sep 19, 2019

YeastCyc has undergone a major overhaul in this release.

Annotation update: YeastCyc was created in 2002 based on partial genome annotation available at the time. The genome annotation in the database was updated in 2013, resulting in a dramatic increase in the number of polypeptides from 837 to 5876. For this release we performed another major update of the annotation from SGD, from UniProt, and from the experimental literature. The product names of 3093 proteins were updated, and we created 774 new polypeptides to bring the number of polypeptides to 6610.

Protein complexes: We imported protein complex data for YeastCyc from the Complex Portal of the European Bioinformatics Institute (EMBL-EBI), bringing the number of protein complexes to 738.

Database synchronization: We propagated cumulative changes in MetaCyc compounds and reactions into YeastCyc, synchronizing the two databases.

Re-evaluation of Pathways: Folloing the annotation update, the pathway prediction algorithm of Pathway Tools was run again on YeastCyc, and the resulting recommendations were reviewed manually by SRI curators, resulting in prediction of several new pathways. Combined with newly curated pathways, we added 58 new pathways. We also re-evaluated the existing pathways, resulting in the removal of 38 pathways. Following these changes, the total number of pathways increased by 20, from 292 to 312.

Transporters: We added transport reactions to 181 transporters not previously associated with any reactions, bringing the total number of transporters associated with transport reactions to 237. We thank the Yeast Transport Protein database (YTPdb) for its useful information.

New Pathways

New Superpathways Revised Pathways

Release Notes for YeastCyc Version 21.5

Released on Nov 28, 2017

Since the last release we have added 3 new pathways to YeastCyc and updated the curation of 12 enzymes. We have also updated the database to contain recent updates to MetaCyc metabolites and reactions.

New Pathways

Updated Enzymes

Release Notes for YeastCyc Version 21.1

Released on Aug 15, 2017

Since the last release we have added 3 new pathways to YeastCyc and updated the curation of nine enzymes. We have also updated the database to contain recent updates to MetaCyc metabolites and reactions.

New Pathways

Updated Enzymes

Release Notes for YeastCyc Version 20.5

Released on Dec 16, 2016

Since the last release we have added 34 new pathways to YeastCyc and revised 2 existing pathways, for a total of 36 new and revised pathways. We have also updated the database with recent changes in MetaCyc.

New Pathways

  • 1,3-β-D-glucan biosynthesis
  • 3-phosphoinositide biosynthesis
  • 4-hydroxyphenylpyruvate biosynthesis
  • acyl carrier protein activation
  • acyl-CoA hydrolysis
  • CMP phosphorylation
  • D-galactose degradation V (Leloir pathway)
  • D-gluconate degradation
  • diphthamide biosynthesis
  • fatty acid beta-oxidation V (unsaturated, odd number, di-isomerase-dependent)
  • formate assimilation into 5,10-methylenetetrahydrofolate
  • formate oxidation to CO2
  • fructose 2,6-bisphosphate biosynthesis
  • glutathione-glutaredoxin redox reactions
  • glycerophosphodiester degradation
  • L-malate degradation II
  • L-methionine biosynthesis
  • methylglyoxal degradation V
  • phosphate acquisition
  • phosphatidylinositol biosynthesis II (eukaryotes)
  • protein S-nitrosylation and denitrosylation
  • pyrimidine deoxyribonucleotide phosphorylation
  • pyrimidine deoxyribonucleotides biosynthesis from CTP
  • pyrimidine nucleobases salvage I
  • pyrimidine ribonucleosides salvage I
  • pyrimidine ribonucleosides salvage III
  • (R)-acetoin biosynthesis I
  • S-adenosyl-L-methionine cycle II
  • stearate biosynthesis I (animals and fungi)
  • sucrose degradation III (sucrose invertase)
  • UDP-D-galactose biosynthesis
  • UMP biosynthesis II
  • urea cycle
  • UTP and CTP dephosphorylation II

    Updated Pathways

  • chitin biosynthesis
  • formate assimilation into 5,10-methylenetetrahydrofolate


    Release Notes for YeastCyc Version 19.1

    Released on June 25, 2015

    Two pathways have been revised during this release. Updated Pathways

  • glycogen degradation II
  • protein N-glycosylation


    Release Notes for YeastCyc Version 18.5

    Released on Nov 7th, 2014

    One new primary pathway has been added during this release. Only a truncated version of the γ-glutamyl cycle comprising the overall biosynthetic and degradation steps of glutathione operates in Saccharomyces cerevisiae. The new pathway, coined DUG (Defective in Utilization of Glutathione) pathway, describes the catalytic reactions involved in the degradation of glutathione. The cytosolic DUG pathway appears to be essential for the maintenance of glutathione homeostasis in the cell and rules out the involvement of the only other glutathione degrading enzyme in yeast, i.e. the vacuolar gamma-glutamyl transpeptidase encoded by ECM38 in this process. New Pathways

  • glutathione degradation (DUG pathway - yeast)


    Release Notes for YeastCyc Version 18.0

    Released on March 24, 2014

    Since the last release 9 new pathways and 2 new superpathways have been added to YeastCyc. Furthermore, 2 existing pathways were extensively revised by adding new gene and enzyme information and updating the respective pathway commentary.

    The new primary metabolic pathways added to YeastCyc include the biosynthesis of fatty acids, cofactors and vitamin B1 derivatives (thiamine triphosphate). Lipoate is an essential sulfur-containing cofactor that is responsible for the lipoylation of the E2 subunits of mitochondrial enzymes involved in mitochondrial maintenance and respiratory growth in yeast. The biosynthesis and incorporation of lipoate has been depicted for three mitochondrial enzymes, i.e. pyruvate dehydrogenase, α-ketoglutarate dehydrogenase and the glycine cleavage enzyme which catalyze the oxidative decarboxylation of glycolysis end products and TCA cycle intermediates, hence connecting cytosolic glycolysis with mitochondrial respiration. The pathway for the direct precursor of lipoate, i.e. octanoyl-[acp] has also been added to YeastCyc. This pathway takes place in the mitochondria and is catalyzed by individual type II fatty acid synthases.

    Other yeast pathways describe the remodeling of phospholipids, e.g. phosphoethanolamine, phosphatidylcholine and phsophatidate involved in the homeostasis of cell membrane glycerophospholipids, as well as a pathway illustrating the metabolism of main precursor monoacylglycerols. Another pathway involved in the integrity and functioning of cell membranes, the sterol:steryl ester interconversion, has also been characterized. This pathway controls the amount of free sterols present in the cell which are available for incorporation into cell membranes. Thiamin (vitamin B1) and its phosphate derivative are involved in many aspects of cellular metabolism. The new pathway describes the synthesis of thiamin triphosphate which apparently does not act as a cofactor but may be involved in protein activation and mediator in signaling pathways. New Pathways

  • lipoate biosynthesis and incorporation (glycine cleavage system, yeast)
  • lipoate biosynthesis and incorporation (pyruvate dehydrogenase and oxoglutarate dehydrogenase, yeast
  • monoacylglycerol metabolism (yeast)
  • octanoyl-[acp] biosynthesis (mitochondria, yeast)
  • phospholipid remodeling (phosphatidate, yeast)
  • phospholipid remodeling (phosphatidylcholine, yeast)
  • phospholipid remodeling (phosphatidylethanolamine, yeast)
  • sterol:steryl ester interconversion (yeast)
  • thiamin triphosphate metabolism

    New Superpathways

  • superpathway of lipoate biosynthesis and incorporation (PDH, KGDH, GCV, yeast)
  • superpathway of phosphatidate biosynthesis (yeast)

    Updated Pathways

  • triacylglycerol degradation
  • triacylglycerol biosynthesis

     

    Release Notes for YeastCyc Version 17.5

    Released on Ocrober 11, 2013

    Since the last release 14 new pathways have been added to YeastCyc. Furthermore, 4 existing pathways were extensively revised by adding new gene and enzyme information and updating the respective pathway commentary. The new primary metabolic pathways added to YeastCyc include the biosynthesis and degradation of fatty acids and vitamin B1 (thiamine).

    Fatty acids fulfill many essential functions in plants, animals and fungi. They determine membrane composition, integrity, and function, are involved in signaling pathways, participate in post-translational protein modification and serve as energy substrates. Yeast can grow on fatty acids as sole carbon source. Saturated fatty acids are completely degraded in the yeast peroxisomal β-oxidation cycle but activated unsaturated fatty acids with cis-, and/or cis/trans-double bonds at odd-numbered positions entail the involvement of so-called auxiliary enzymes which are employed in various pathways to utilize oleoyl-CoA, 10-cis/trans-heptadecenoyl-CoA and 9-cis,11-trans-octadecenoyl-CoA. In addition, the pathway describing the unique regulation of phosphatidylglycerol, a biosynthetic intermediate of the major anionic mitochondrial phospholipid cardiolipin has been added. Another new pathway delineates a resynthesis pathway of phosphatidylcholine, an important eukaryotic membrane phospholipid, operating supplemental to the two known biosynthetic routes for phosphatidylcholine formation in yeast.

     Thiamine (vitamin B1) and its phosphate derivatives are involved in many aspects of cellular metabolism, e.g. as indispensable co-factor in carbohydrate and amino acid catabolism. The new pathways describe the synthesis of the pyrimidine moiety in yeast which differs from both animal and plant pathways, and additional salvage pathways of thiamine catalyzed by bifunctional (TMP diphosphorylase/hydroxyethylthiazole kinase THI6) and trifunctional (HMP/HMP-P kinase/thiaminase II THI20) enzymes. The latter has even the enzymatic scope to catalyze the hydrolytic cleavage of synthetic antagonists, i.e. pyrithiamine and oxythiamine for the formation of thiamine in yeast.

    New Pathways
  • 4-amino-2-methyl-5-phosphomethylpyrimidine biosynthesis
  • 4-methyl-5(β-hydroxyethyl)thiazole salvage
  • 9-cis,11-trans-octadecadienoyl-CoA degradation (isomerase-dependent)
  • 10-cis-heptadecenoyl-CoA degradation
  • 10-trans-heptadecenoyl-CoA degradation (MFE-dependent)
  • 10-trans-heptadecenoyl-CoA degradation (reductase-dependent)
  • fatty acid beta-oxidation (peroxisome)
  • oleate beta-oxidation (isomerase-dependent)
  • oleate beta-oxidation (reductase-dependent)
  • oleate beta-oxidation (thioesterase-dependent)
  • phosphatidylcholine resynthesis via glycerophosphocholine
  • phosphatidylglycerol degradation
  • thiamin formation from pyrithiamine and oxythiamine
  • thiamin salvage IV

     

    Updated Pathways

  • base-degraded thiamin salvage
  • dehydro-D-arabinono-1,4-lactone biosynthesis
  • pyridoxal 5'-phosphate biosynthesis II
  • thiazole biosynthesis III (eukaryotic)

     

    Release Notes for YeastCyc Version 17.1

    Released on June 11, 2013

    Since the last release 11 new pathways and 2 new super pathways have been added to YeastCyc. Furthermore, 8 existing pathways were extensively revised by adding new gene and enzyme information and updating the respective pathway commentary. The new primary metabolic pathways added to YeastCyc include the biosynthesis of Coenzyme Q6 (ubiquinol-6), which is formed by a multi-subunit complex and functions in the electron transport chain in mitochondria. Besides its role as a redox-active component in the respiratory chain Coenzyme Q functions as membrane antioxidant and cofactor of uncoupling proteins.

    The pyridine nucleotides NADH and NADPH play pivotal roles in energy metabolism, electron transfer, and indispensable metabolic cycles of yeast as well as in the maintenance of the cellular redox status and participation in signaling pathways. In this release we added the pathways delineating the interconversion of the major oxidized and reduced forms NAD/NADH and NADP/NADPH in mitochondria and the cytosol, which are carried out by different sets of enzymes.

    Another addition for this release was the yeast aerobic respiration pathway, which differs from the plant and animal version by the absence of complex I.

    New Pathways
  • adenosine deoxyribonucleotides de novo biosynthesis I
  • adenosine ribonucleotides de novo biosynthesis
  • aerobic respiration (cytochrome c)
  • guanine and guanosine salvage I
  • guanosine deoxyribonucleotides de novo biosynthesis I
  • guanosine ribonucleotides de novo biosynthesis
  • iron-sulfur cluster biosynthesis
  • NAD/NADP-NADH/NADPH cytosolic interconversion
  • NAD/NADP-NADH/NADPH mitochondrial interconversion
  • ubiquinol-6 biosynthesis from 4-aminobenzoate
  • ubiquinol-6 bypass biosynthesis

    New Superpathways

  • superpathway NAD/NADP-NADH/NADPH interconversion
  • superpathway of ubiquinol-6 biosynthesis

    Updated Pathways

  • aerobic respiration (linear view)
  • β-alanine biosynthesis
  • coenzyme A biosynthesis
  • phosphopantothenate biosynthesis I
  • putrescine biosynthesis III
  • spermidine biosynthesis I
  • spermine biosynthesis
  • ubiquinol-6 biosynthesis from 4-hydroxybenzoate

     

    Release Notes for YeastCyc Version 17.0

    Released on March 28, 2013

    Several major changes have happened in this release.

    Since its creation in 2002 and until 2013 YeastCyc has been developed solely by SGD curators. During that period YeastCyc has diverged significantly from other BioCyc databases due to parallel creation of compounds, reactions and pathways. This has led to difficulties in comparing the metabolism of Saccharomyces cerevisiae with that of other organisms included in the BioCyc collection.

    In early 2012 the database was moved to SRI International, where it will be curated by both SGD curators and SRI curators. Several projects accompanied the transition:

    Genome Update: The Saccharomyces cerevisiae genome used for generating the original database was only partially annotated, leading to many missing genes. The genome annotation has now been updated, resulting in a dramatic increase in the number of polypeptides from 837 to 5876.

    Database synchronization: A significant effort was spent synchronizing the compounds, reactions and pathways between YeastCyc and MetaCyc, resulting in full synchronization of compounds and reactions, and much increased synchronization of pathways.

    Re-evaluation of Pathways: The pathway prediction algorithm of Pathway Tools was run again on YeastCyc, and the resulting recommendations were reviewed manually by SRI curators, resulting in replacement of many of the existing pathways with more current pathways from MetaCyc, as well as incorporation of many new pathways. Existing pathways that have been created especially for S. cerevisiae by SGD curators that were deemed more appropriate than the MetaCyc pathways were left in the database. The total number of pathways increased from 154 to 239.

    Change of version numbers: From now on the version number of YeastCyc will be the same as the version numbers of all other BioCyc databases.