New features

Please refer to our recent publication describing the Arabidopsis Leaf Quantitative Atlas, (PMID:38572078). This work shows how quantitative data extracted from ChloroKB and integrated with cellular/subcellular volumes can be used to calculate concentrations (to constraint quantitative models for example). If you are interested in the quantitative_data.csv export file, please open it with Notepad++, then copy and paste in e.g. Excel for correct representation of the greek symbols in metabolite names.

New content

This eleventh release contains 218 new reviewed proteins, represented in 28 new maps.

• The synthesis of the last missing cofactor-Molybdopterin cofactor, or MoCo- is now available (Molybdopterin MoCo synthesis) along with a detailed representation of the sophisticated biochemistry of molybdopterin synthesis and Mo insertion (Molybdopterin synthase Mo insertase).
• The major part of the present release contains the reconstruction of transport processes in a generic cell at the plasma membrane and intracellularly for iron, malate, nucleosides, polyamines and the 20 amino acids:
• Iron transport.
• Malate transport.
• Nucleosides transport.
• Polamines transport.
• An overview of the 102 proteins involved or potentially involved in amino acids trafficking, with still many unknown substrates or localization: L-amino acids transport. 20 maps for each amino acids were built and are accessible by clicking on the corresponding icons at the bottom of the L-amino acids transport map.
• Iron trafficking is completed with a map describing iron storage in a generic Arabidopsis cell (Iron storage).

New content

This tenth release contains eight new or revised maps containing 89 new reviewed proteins, representing nitrate transport, ammonium transport and its regulation, as well as other regulatory processes. The Nitrate transport map is the principal part of this 10^th update with an exhaustive representation of the molecular actors of nitrate transport at the cellular level (in a generic cell), with 47 proteins involved, among which 32 are well-characterized and 15 still await biochemical/genetic characterizations.

• Links to the eight new maps:
• Nitrate_transport
• Ammonium_transport_regulation
• For clarity reasons, the previous map related to ADP-glucose pyrophosphorylase activity was split in two maps, one representing the enzymes: ADP_glucose_pyrophosphorylases and a second one focusing on the multi-level regulation of the enzyme activity: ADP_glucose_pyrophosphorylase_regulation
• NAD and NADH kinases are now represented in a dedicated map rather than embedded in the NAD synthesis map: NAD_NADH_kinases
• Pyruvate kinases and Pyruvate Phosphate Dikinase (PPDK) are represented with additional maps describing the details of their regulation: Pyruvate_kinases, Pyruvate_kinases_regulation, Pyruvate_Phosphate_dikinase, Pyruvate_Phosphate_dikinase_regulation
• The maps available in ChloroKB cannot be all displayed in the Welcome page; a special map was designed allowing to figure out the extent of the reconstruction: (see All_maps).

New features

A complete stoichiometry matrix of the reconstructed network can be downloaded (download icon on the welcome page).

The quantitative data document was improved with hyperlinks, chemical identifiers, source biological material and the compartment where the metabolite was quantified. The document can be exported as a csv file.

Cross references: The MASCP Gator link is not anymore active; please use the peptideAtlas link.

New content

This ninth release contains 68 new reviewed proteins, represented in six new maps representing additional processes in lipid metabolism in the endoplasmic reticulum (ER) and the mitochondrion.

• For an overview of lipid synthesis see Lipids synthesis overview. The map is also accessible from the home page (bottom right). The links to the five new maps are:
• Fatty_acids_synthesis_mitochondrion
• Very_long-chain fatty acids synthesis
• Extra-long-chain_fatty_acids_synthesis
• Desaturation_by_ADSs
• Triacylglycerols synthesis
• Triacylglycerols_catabolism.
• The sulfate assimilation map is now completed with sulfate transporters at the plasma membrane and at the tonoplast (see Sulfate assimilation).

New features

A stoichiometric matrix of the reconstructed network can be optained by clicking the downloadable document icon in the welcome page.

New content

This eighth release contains 68 new reviewed proteins, represented in twelve new maps focusing on lipid synthesis in the endoplasmic reticulum (ER) and lipid trafficking between the ER and the plastid.

• For an overview of lipid synthesis see Lipids synthesis overview. The map is also accessible from the home page (bottom right). The links to the twelve new maps are:
• Phosphatidic acid synthesis ER (detailed)
• CDP-diacylglycerol synthesis (major species)
• Phosphatidylinositol synthesis
• Diacylglycerol synthesis ER
• Diacylglycerol transfer to plastid
• Head group synthesis of PC and PE: Phosphatidylcholine Phosphatidylethanolamine syntheses
• Phosphatidylcholine synthesis (detailed)) and a tentative representation of CCT1 regulation Choline-phosphate cytidylyltransferase 1 regulation
• Phosphatidylcholine desaturation
• Phosphatidylethanolamine synthesis (detailed)
• Acyl-editing.
• A map is dedicated to fatty acid transport into the peroxisome, (Acyl-CoA transport peroxisome), thus connecting lipids synthesis and degradation by β-oxidation (see the links in the fourth release).

New features

In this release, the display in the molecule description pages (proteins, metabolites, chemical inhibitors, complexes) was modified and the screen space use was optimized. Icons of maps containing the molecule queried are represented together with their names. The names of the metabolic maps also appear when sliding the mouse over the map icons.

New content

This seventh release contains 2 new maps: one is dedicated to Sugar transport (sucrose, glucose, maltose etc.) and the other to Polyol transport (Sorbitol, xylitol etc. ), at the cellular level. Please note that sugar transport is cell specific; the sugar transport map represents a generic cell; comments in the map (grey ovals) provide indications of the cell type where the transporters are expressed.

New features

The different kind of reactions in ChloroKB can now be searched using the following keywords: "transport", "RXN" and "NotInMetacyc". There are 379 transport reactions, 1136 reactions with MetaCYC identifiers and 258 reactions for which identifiers could not be found in MetaCYC.

New content

This sixth release contains 152 new reviewed proteins, represented in 11 new maps. Quantitative data for many metabolites can be downloaded.

Metabolic pathways:

• lipid synthesis: see Long-chain acyl-CoA synthesis
• L-ascorbate metabolism: the implication of L-ascorbate in H₂O₂ detoxification and its extra cellular metabolism are represented in L-ascorbate glutathione pathway and L-ascorbate apoplastic metabolism, respectively.
• Glutathion metabolism : see Glutathione degradation
• CO₂ conversion into bicarbonate : see CO₂ and carbonic anhydrases
• Acetyl-CoA metabolism in the cytosol, peroxisome and mitochondrion is now represented with a specific hub map (Acetyl-CoA HUB cytosol). Chloroplastic acetyl-CoA metabolism previously available can be found here: Acetyl-CoA HUB chloroplast
• The plant-specific alternative electron transfer chain with external and internal type II NAD(P)H dehydrogenases, Ca²⁺ regulation of NDB1, and alternative oxidases is represented here: Alternative electron transfer chain. The regulation of alternative oxidase AOX1A by oxidation/reduction and organic acid activation is detailed here: Alternative oxidase regulation
• Transport at the plasma membrane is still poorly represented in ChloroKB, an exception is phosphate transport now avaibable: Phosphate transport.
• A tentative representation of the detoxidication of aldehydes and ketones molecules deriving from polyunsaturated fatty acids in two maps : Long chain aldehydes and Short chain aldehydes and ketones.

New features

See the second release (below) on March 6^th, 2018

New content

This fifth release contains 39 new reviewed proteins, represented in 4 new maps. With this release, we completed the reconstruction of starch metabolism (synthesis and degradation).

Metabolic pathways:

• Starch initiation: see Starch initiation
• Amylopectin synthesis: see Starch (amylopectin) synthesis
• Amylose synthesis from pre-amylopectin : see Starch (amylose) synthesis
• Starch degradation : see Starch degradation
• In addition, the ATP ADP AMP adenosine map was simplified with the creation of a new map dedicated to the transport of these species between compartments : see ATP ADP AMP transport
• Finally, a bug was corrected allowing access to a map describing the glyoxylate cycle: see Glyoxylate cycle

New content

This fourth release contains 56 new reviewed proteins (total 1329), represented in 15 new maps (total 171 maps).

Metabolic pathways:

• Arginine degradation and transformation into polyamine precursors: see L-arginine transformation
• Branched-chain amino-acid degradation (still incompletely characterized in plant) with three specific maps: see L-isoleucine degradation, L-leucine degradation, L-valine degradation.
• Beta-oxidation is represented for saturated and unsaturated fatty acids in an explicit manner (i.e. all intermediate molecules and branches are represented): see Saturated fatty acids beta-oxidation, Linoleoyl-CoA beta-oxidation, Linolenoyl-CoA beta-oxidation, Oleoyl-CoA beta-oxidation, cis-vaccenoyl-CoA beta-oxidation.

New detailed regulatory processes:

• The six 2-ketoacid dehydrogenases are all represented: see Branched-chain Isoleucine ketoacid decarboxylase, Branched-chain_leucine_ketoacid_decarboxylase, Branched-chain_valine_ketoacid_decarboxylase, Mitochondrial Pyruvate dehydrogenase and its regulation by metabolites and phosphorylation Mitochondrial Pyruvate dehydrogenase regulation, Plastidial Pyruvate dehydrogenase and oxoglutarate dehydrogenase, already available since the previous release, see Oxoglutarate dehydrogenase.

New content

ChloroKB reconstructed metabolic network now extends far beyond chloroplast metabolism; In this third release, the representation of the synthesis of organic acids by the mitochondrion and the cytosol is completed. 89 new proteins are represented in 8 new maps and some maps have been modified (e.g. L-aspartate metabolism is represented in a single map, L-aspartate, showing the different functions of L-aspartate in the chloroplast-mainly used as a precursor-and in the other compartments, where it is involved for example in the Aspartate-Glutamate shuttle during photorespiration).

Metabolic pathways:

• Addition of the TCA cycle, functionally associated with the GABA shunt: see TCA cycle and GABA shunt

New HUBS:

• Two new hubs are available, centered on citrate (see Citrate HUB) and oxaloacetate (see Oxaloacetate HUB).

New detailed regulatory processes:

• Five new maps describing enzyme complexes and associated regulatory processes have been added, see Oxoglutarate dehydrogenase, PEP Carboxykinase regulation, PEP Carboxylase regulation, Glutamate decarboxylase 1 regulation, and Succinate dehydrogenase.

Second release, March 6^th, 2018

New features

Multidomain proteins are now graphically represented

This new feature allows to distinguish two kinds of multifunctional proteins: the ones that catalyze different reactions in the same active site (e.g. Aspartate/Prephenate aminotransferase in L-tyrosine and L-phenylalanine map) from the ones with several domains catalyzing a given reaction (e.g. the protein PHYLLO in Phylloquinone synthesis). This also allows the representation of proteins with regulatory domains (see for example the Aspartate kinases map).

Physiological direction of reversible reactions

The double arrows symbolizing reversible reactions in CellDesigner are now represented with a white and a black end: the black end points towards the presumed physiological direction of the flux in leaf (see for example the aspartate kinase step in the L-lysine and L-threonine map).

New content

87 new reviewed proteins are represented in 22 new maps.

Metabolic pathways:

• Lipid synthesis in the chloroplast is now completed (see lipids synthesis overview) with 12 detailed maps (e.g. fatty acids synthesis, fatty acids export, phosphatidylglycerol synthesis, desaturation processes, etc…).
• Glyoxal and methylglyoxal detoxification
• Vitamin B9 metabolism is now completed with tetrahydrofolates interconversions
• Chlorophyll synthesis is linked to Chlorophyll degradation

Some extra-chloroplastic processes are being represented:

• Cardiolipin synthesis in the mitochondrion

New hubs:

• Malate HUB
• Pyruvate_HUB_cytosol
• Isocitrate_HUB

New detailed regulatory processes:

• The regulation of chloroplastic NADP malate dehydrogenase: see NADP-malate dehydrogenase
• The complex control of the mitochondrial NAD–malic enzymes by CoA and fumarate: see NAD–malic enzymes

Last update: September 2024 - Contact: chlorokb(at)cea