Fungal ammonium assimilation into glutamate and glutamine, and glutamate deamination

Assimilation of ammonium into the amino group of L-glutamate and the amide group of L-glutamine, and the reverse release of ammonium from glutamate, as organised in fungi and other eukaryotic microbes. Glutamate and glutamine are the nitrogen donors for nearly all other nitrogenous compounds, so these reactions sit between nitrogen-source catabolism and biosynthesis. Glutamine synthetase ligates ammonium to L-glutamate with ATP to give L-glutamine; it is the only route to glutamine and is required in every growth condition. Ammonium reaches glutamate by two alternative routes. In the first, NADP-dependent glutamate dehydrogenase reductively aminates 2-oxoglutarate with NADPH; in budding yeast this is the main route when glucose is plentiful and is carried by two isozymes, one constitutive and one induced on non-fermentable carbon sources. In the second, the glutamine synthetase-glutamate synthase (GS-GOGAT) cycle, an NADH-dependent glutamate synthase transfers the glutamine amide nitrogen to 2-oxoglutarate, giving two molecules of L-glutamate, one of which replaces the glutamate consumed by glutamine synthetase. Fungal glutamate synthase is a single large polypeptide that combines the domains carried by the separate large and small subunits of bacterial NADPH-dependent glutamate synthase. The GS-GOGAT cycle has higher affinity for 2-oxoglutarate and uses NADH rather than NADPH, and it becomes required for glutamate synthesis when the NADP-dependent dehydrogenases are absent or when glutamine is the nitrogen source. Loss of both routes causes glutamate auxotrophy. An NAD-dependent glutamate dehydrogenase runs the reaction in the catabolic direction, oxidatively deaminating L-glutamate to 2-oxoglutarate and ammonium; it supplies the ammonium for glutamine synthesis when glutamate is the nitrogen source. 2-Oxoglutarate itself comes from isocitrate dehydrogenases of central carbon metabolism.

MODULE:nitrogen_assimilation_glutamate_glutamineDRAFTMetabolic Pathwaymodules/nitrogen_assimilation_glutamate_glutamine.yaml
L-glutamate biosynthetic processGO:0097054 L-glutamine biosynthetic processGO:1901704
YeastPathways:PWY3O-13
superpathway of glutamate biosynthesis (S. cerevisiae, SGD YeastPathways)
Source superpathway: GLUTDEHYD-RXN (GDH1, GDH3), GLUTAMINESYN-RXN (GLN1), GLUTAMATE-SYNTHASE-NADH-RXN (GLT1) and ISOCITDEH-RXN (IDP1, IDP2, IDP3). The glutamate and glutamine reactions are modelled; the isocitrate dehydrogenase reaction is 2-oxoglutarate supply and is kept outside the module.
YeastPathways:GLUNH3-PWY
glutamate biosynthesis from ammonia (S. cerevisiae, SGD YeastPathways)
NADP-dependent glutamate dehydrogenase reaction (GDH1, GDH3); both assignments retained.
YeastPathways:GLNSYN-PWY
L-glutamine biosynthesis I (S. cerevisiae, SGD YeastPathways)
Glutamine synthetase reaction (GLN1); assignment retained.
YeastPathways:GLUGLNSYN-PWY
L-glutamate biosynthesis IV (S. cerevisiae, SGD YeastPathways)
NADH-dependent glutamate synthase reaction (GLT1); assignment retained.
YeastPathways:PWY-3322
glutamate degradation IX (S. cerevisiae, SGD YeastPathways)
NAD-dependent glutamate dehydrogenase reaction (GDH2) in the catabolic direction; assignment retained.
GO:0097054
L-glutamate biosynthetic process
Module-level biological process.
GO:1901704
L-glutamine biosynthetic process
Module-level biological process (glutamine synthetase step).
GO:0019676
ammonia assimilation cycle
Biological process of the GS-GOGAT route.
GO:0006538
L-glutamate catabolic process
Biological process of the NAD-dependent glutamate deamination part.
PMID:14555464
Ammonia assimilation by Saccharomyces cerevisiae.
Review of the two assimilation routes in yeast: NADPH-dependent glutamate dehydrogenase sets the growth rate on glucose plus ammonia, whereas the NADH-dependent GS-GOGAT route is favoured when 2-oxoglutarate is low.
the rate of growth is determined by the ability of the cell to use glutamate dehydrogenase to assimilate ammonia and is not affected by mutations resulting in the loss of glutamate synthase
PMID:22419079
Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae.
Review: GDH1 and GLN1 assimilate ammonium on glucose, GDH3 contributes on ethanol, GLT1 is required when glutamine is the sole nitrogen source, and GDH2 releases ammonium from glutamate. Cited by YeastPathways for PWY3O-13.
PMID:11562373
NADP-glutamate dehydrogenase isoenzymes of Saccharomyces cerevisiae. Purification, kinetic properties, and physiological roles.
Purified Gdh1 and Gdh3 are both biosynthetic NADP-dependent glutamate dehydrogenases with different allosteric properties and differential carbon-source regulation; Gdh2 is the catabolic NAD-dependent enzyme.
two NADP(+)-dependent glutamate dehydrogenases (NADP-GDHs) encoded by GDH1 and GDH3 catalyze the synthesis of glutamate from ammonium and alpha-ketoglutarate
PMID:9287019
GDH3 encodes a glutamate dehydrogenase isozyme, a previously unrecognized route for glutamate biosynthesis in Saccharomyces cerevisiae.
gdh1 glt1 double mutants still grow on ammonium because of GDH3; the gdh1 glt1 gdh3 triple mutant is a glutamate auxotroph, showing that the NADP-GDH and GOGAT routes are the only routes of glutamate synthesis.
Triple mutants impaired in GDH1, GLT1, and GDH3 were obtained. These were strict glutamate auxotrophs.
PMID:2570348
Three regulatory systems control expression of glutamine synthetase in Saccharomyces cerevisiae at the level of transcription.
GLN1 is the S. cerevisiae glutamine synthetase structural gene.
The GLN1 gene of Saccharomyces cerevisiae was cloned by complementation of a gln1 auxotroph.
PMID:8923741
Sequence of the GLT1 gene from Saccharomyces cerevisiae reveals the domain structure of yeast glutamate synthase.
Yeast glutamate synthase is a homotrimer of a 199 kDa GLT1 polypeptide carrying glutamine-, FMN-, NADH- and iron-sulfur-binding regions homologous to the bacterial and plant enzymes.
this enzyme is a homotrimeric protein with a monomeric size of 199 kDa
PMID:9657994
Regulation of expression of GLT1, the gene encoding glutamate synthase in Saccharomyces cerevisiae.
GLT1 is repressed by glutamate and activated by Gln3 and Gcn4; on ammonium GOGAT is an ancillary route of glutamate synthesis.
Our results suggest that in a wild-type strain grown on ammonium, GOGAT constitutes an ancillary pathway for glutamate biosynthesis.
PMID:1975578
Role of NAD-linked glutamate dehydrogenase in nitrogen metabolism in Saccharomyces cerevisiae.
GDH2 encodes the NAD-linked glutamate dehydrogenase, the main route that releases ammonia from glutamate; it is not normally used for glutamate synthesis.
Our results indicate that the NAD-linked glutamate dehydrogenase catalyzes the major, but not sole, pathway for generation of ammonia from glutamate.
PMID:1652057
Physiological and genetic analysis of the carbon regulation of the NAD-dependent glutamate dehydrogenase of Saccharomyces cerevisiae.
GDH2 expression is regulated by the carbon source as well as by nitrogen; cited by YeastPathways for PWY-3322.
PMID:7773104
Glutamine synthetase/glutamate synthase ammonium-assimilating pathway in Schizosaccharomyces pombe.
S. pombe has the same two assimilation routes: gln1 mutants lacking glutamine synthetase are glutamine auxotrophs, and only mutants lacking both GOGAT and NADP-GDH fail to grow on ammonium.
Double-mutant strains containing gog1-1 and gdh1-1 or gdh2-1 (mutations that result specifically in the abolition of NADP-GDH activity) result in a complete lack of growth on ammonium as sole nitrogen source
PMID:15574419
Kinetic properties and metabolic contributions of yeast mitochondrial and cytosolic NADP+-specific isocitrate dehydrogenases.
Mitochondrial NAD-IDH (IDH1/IDH2) carries the major isocitrate flux and supplies the 2-oxoglutarate pool in glucose-grown cells, and IDP2 does so on non-fermentable carbon; loss of IDH causes glutamate auxotrophy.
A substantial cellular pool of alpha-ketoglutarate is attributed to IDH function during glucose growth
PMID:8672488
Expression and gene disruption analysis of the isocitrate dehydrogenase family in yeast.
Any one of the three yeast isocitrate dehydrogenases (mitochondrial NAD, mitochondrial NADP or cytosolic NADP) is enough for glutamate-independent growth, so 2-oxoglutarate supply is a redundant upstream input rather than a single pathway step.
expression of at least one isozyme is necessary for glutamate-independent growth
6Nodes
3Parts
1Variant Sets
2Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:nitrogen_assimilation_glutamate_glutamine deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • glutamine_synthetase_step → gs_gogat_route [NOT_CHECKED]
  • glutamate_formation → glutamine_synthetase_step [NOT_CHECKED]
  • glutamate_deamination_step → glutamine_synthetase_step [NOT_CHECKED]

Function consistency and core coverage

9 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (13 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
glutamine_synthetase_activity GLN1 (Saccharomyces cerevisiae)
UniProtKB:P32288
Family Representative 		glutamine synthetase activity
GO:0004356 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
glutamine_synthetase_activity gln1 (Schizosaccharomyces pombe)
UniProtKB:Q09179
Family Representative 		glutamine synthetase activity
GO:0004356 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nadp_glutamate_dehydrogenase_activity GDH1 (Saccharomyces cerevisiae)
UniProtKB:P07262
Family Representative 		L-glutamate dehydrogenase (NADP+) activity
GO:0004354 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nadp_glutamate_dehydrogenase_activity GDH3 (Saccharomyces cerevisiae)
UniProtKB:P39708
Family Representative 		L-glutamate dehydrogenase (NADP+) activity
GO:0004354 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nadp_glutamate_dehydrogenase_activity gdh1 (Schizosaccharomyces pombe)
UniProtKB:P78804
Family Representative 		L-glutamate dehydrogenase (NADP+) activity
GO:0004354 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nadh_glutamate_synthase_activity GLT1 (Saccharomyces cerevisiae)
UniProtKB:Q12680
Family Representative 		glutamate synthase (NADH) activity
GO:0016040 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nadh_glutamate_synthase_activity glt1 (Schizosaccharomyces pombe)
UniProtKB:Q9C102
Family Representative 		glutamate synthase (NADH) activity
GO:0016040 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nad_glutamate_dehydrogenase_activity GDH2 (Saccharomyces cerevisiae)
UniProtKB:P33327
Family Representative 		L-glutamate dehydrogenase (NAD+) activity
GO:0004352 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
nad_glutamate_dehydrogenase_activity gdh2 (Schizosaccharomyces pombe)
UniProtKB:Q9USN5
Family Representative 		L-glutamate dehydrogenase (NAD+) activity
GO:0004352 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
glutamine_synthetase_activity eukaryotic type II glutamine synthetases
PANTHER:PTHR20852:SF57
Family 		glutamine synthetase activity
GO:0004356 		Family Supported
Family review supports GO:0004356 FAMILY_WIDE. Asserted by glutamate_glutamine_ammonia_hub; accepted by GLN1, gln1 and GLUL.
nadp_glutamate_dehydrogenase_activity hexameric NADP-specific glutamate dehydrogenases
PANTHER:PTHR43571:SF1
Family 		L-glutamate dehydrogenase (NADP+) activity
GO:0004354 		Family Supported
Family review supports GO:0004354 FAMILY_WIDE. Accepted by every reviewed member (GDH1, GDH3, gdh1, gdhA).
nadh_glutamate_synthase_activity single-chain NADH-dependent glutamate synthases
Family 		glutamate synthase (NADH) activity
GO:0016040 		Family Id Missing
The family has no identifier linking it to a curated family review.
nad_glutamate_dehydrogenase_activity large NAD-specific glutamate dehydrogenases
PANTHER:PTHR11606:SF24
Family 		L-glutamate dehydrogenase (NAD+) activity
GO:0004352 		Family Supported
Family review supports GO:0004352 FAMILY_WIDE. NAD-linked glutamate dehydrogenase activity is shared by every reviewed member (GDH2, gdh2, GLUD1, GLUD2).

Gene-review completeness (9/9 grounded genes reviewed)

9 complete review(s) · 5 with deep research · 0 missing review · 4 reviewed but lacking deep research

Gene Review Complete Deep research
GDH1 P07262 ✓ ✓ ✓
gdh1 P78804 ✓ ✓ ✗
GDH2 P33327 ✓ ✓ ✓
gdh2 Q9USN5 ✓ ✓ ✗
GDH3 P39708 ✓ ✓ ✓
GLN1 P32288 ✓ ✓ ✓
gln1 Q09179 ✓ ✓ ✗
GLT1 Q12680 ✓ ✓ ✓
glt1 Q9C102 ✓ ✓ ✗

Details

Fungal ammonium assimilation into glutamate and glutamine, and glutamate deaminationMetabolic Pathwaynitrogen_assimilation_glutamate_glutamine
L-glutamate biosynthetic processGO:0097054 L-glutamine biosynthetic processGO:1901704

Boundary: ammonium to L-glutamate and L-glutamine, plus the NAD-GDH catabolic reaction that returns glutamate nitrogen to ammonium. 2-Oxoglutarate supply by isocitrate dehydrogenases is upstream central carbon metabolism and belongs to tca_cycle. YeastCyc lists only the NADP isozymes (ISOCITDEH-RXN: IDP1, IDP2, IDP3) and omits the mitochondrial NAD-dependent IDH1/IDH2, which carries the main flux and supplies most of the 2-oxoglutarate pool on glucose, while cytosolic IDP2 dominates on non-fermentable carbon (PMID:15574419). Any one isozyme suffices for glutamate-independent growth (PMID:8672488). IDP3 is peroxisomal and supplies NADPH for beta-oxidation of unsaturated fatty acids, not 2-oxoglutarate for glutamate synthesis. Glutamine-amide transfer to other acceptors, nitrogen-source catabolism and nitrogen catabolite repression (Gln3, Gat1, Ure2, Gcn4) are outside the module. Generalisation: the module is fungal-scope. bacterial_ammonia_assimilation models the bacterial GS-GOGAT cycle, which uses GSI-type GlnA and a two-subunit NADPH-dependent GltB/GltD glutamate synthase (GO:0004355) rather than the GSII-type glutamine synthetase and single-chain NADH-dependent GLT1 of fungi; the chemistry of the cycle conforms. glutamate_glutamine_ammonia_hub is the animal arrangement, which has no glutamate synthase, a dual-cofactor mitochondrial GDH (GO:0004353) and glutaminases; animal GS (GLUL) belongs to the same PANTHER family as fungal GLN1. YeastCyc assessment: gene assignments for GDH1, GDH3, GLN1, GLT1 and GDH2 are correct and no S. cerevisiae enzyme is missing. GO-CAM disagreements: (a) YeastPathways_PWY3O-13 asserts IDP1 (mitochondrial) and IDP3 (peroxisomal) in the cytosol and puts all three isocitrate dehydrogenases part_of GO:0097054; (b) GDH2 has no YeastPathways GO-CAM, because PWY-3322 was not converted; (c) PomBase model 67c10cc400000148 omits gdh1, the NADP-GDH that with GOGAT is required for growth on ammonium (PMID:7773104), and places glt1 and gdh2 in the mitochondrial matrix (see knowledge gap); (d) neither model has causal edges between glutamine synthetase and glutamate synthase. The PomBase model also contains alanine transaminase (alt1), which is modelled in aspartate_asparagine_metabolism, and arginine/lysine entry steps and tRNA ligases, which are outside both modules.

Connections

L-glutamine made by glutamine synthetase is the amide donor for glutamate synthase.
L-glutamate made by either route is the substrate of glutamine synthetase.
On glutamate as nitrogen source, ammonium released by NAD-dependent glutamate dehydrogenase is fixed by glutamine synthetase.
Part 1: glutamine synthesis
L-glutamate + ammonium + ATP to L-glutamineReactionglutamine_synthetase_step
L-glutamine biosynthetic processGO:1901704

Annotons

Glutamine synthetase
glutamine_synthetase_activity
Participant: Family: GLN1 / gln1 (glutamine synthetase)
Gene:
GLN1 / gln1 (glutamine synthetase)
Family:
eukaryotic type II glutamine synthetases Fungal glutamine synthetases are GSII-type enzymes in PANTHER PTHR20852, the family of the animal and plant cytoplasmic enzymes; bacterial GlnA (GSI) is a different PANTHER family (PTHR43407).
Representative Members: GLN1 (Saccharomyces cerevisiae)UniProtKB:P32288 gln1 (Schizosaccharomyces pombe)UniProtKB:Q09179

Function

glutamine synthetase activityGO:0004356
Substrates: L-glutamate ammonium ATP
Products: L-glutamine ADP phosphate

Locations

cytosolGO:0005829

Sole route to L-glutamine and first half of the GS-GOGAT cycle; also fixes the ammonium released by NAD-dependent glutamate dehydrogenase when glutamate is the nitrogen source.

Part 2: ammonium incorporation into glutamate
Ammonium (or glutamine amide) plus 2-oxoglutarate to L-glutamateMetabolic Pathwayglutamate_formation
L-glutamate biosynthetic processGO:0097054
Variant set: Route of nitrogen incorporation into glutamate by enzyme chemistry / assimilation route (One Or More)

Both routes co-exist in S. cerevisiae and S. pombe and either is sufficient for growth on ammonium; loss of both gives glutamate auxotrophy (PMID:9287019, PMID:7773104). Their relative use depends on carbon and nitrogen source (PMID:14555464, PMID:11562373).

Reductive amination by NADP-dependent glutamate dehydrogenaseReactionnadp_gdh_route

Annotons

NADP-dependent glutamate dehydrogenase
nadp_glutamate_dehydrogenase_activity
Participant: Family: GDH1 / GDH3 / gdh1 (NADP-GDH)
Gene:
GDH1 / GDH3 / gdh1 (NADP-GDH)
Family:
hexameric NADP-specific glutamate dehydrogenases
Representative Members: GDH1 (Saccharomyces cerevisiae)UniProtKB:P07262 GDH3 (Saccharomyces cerevisiae)UniProtKB:P39708 gdh1 (Schizosaccharomyces pombe)UniProtKB:P78804

Function

L-glutamate dehydrogenase (NADP+) activityGO:0004354
Substrates: 2-oxoglutarate ammonium NADPH
Products: L-glutamate NADP+

Locations

cytosolGO:0005829

Direct, lower-affinity fixation of ammonium on 2-oxoglutarate using NADPH; the main assimilation route of budding yeast on glucose.

Glutamine amide transfer by NADH-dependent glutamate synthase (GS-GOGAT cycle)Reactiongs_gogat_route
ammonia assimilation cycleGO:0019676

Annotons

NADH-dependent glutamate synthase
nadh_glutamate_synthase_activity
Participant: Family: GLT1 / glt1 (NADH-GOGAT)
Gene:
GLT1 / glt1 (NADH-GOGAT)
Family:
single-chain NADH-dependent glutamate synthases No PANTHER id is asserted. The fungal enzymes are single polypeptides fusing the domains of the bacterial GltB large and GltD small subunits; PANTHER places them in PTHR43100 (named after the small chain), whose label does not describe the fused protein, while E. coli GltB is in PTHR11938.
Representative Members: GLT1 (Saccharomyces cerevisiae)UniProtKB:Q12680 glt1 (Schizosaccharomyces pombe)UniProtKB:Q9C102

Function

glutamate synthase (NADH) activityGO:0016040
Substrates: L-glutamine 2-oxoglutarate NADH
Products: L-glutamate (two molecules) NAD+

Second half of the GS-GOGAT cycle. Uses NADH and has a higher affinity for 2-oxoglutarate than NADP-GDH; required for glutamate synthesis on glutamine or in the absence of NADP-GDH. No compartment is asserted (see knowledge gap).

Part 3: glutamate oxidative deamination (catabolic) (optional)
L-glutamate + NAD+ to 2-oxoglutarate + ammoniumReactionglutamate_deamination_step
L-glutamate catabolic processGO:0006538

Annotons

NAD-dependent glutamate dehydrogenase
nad_glutamate_dehydrogenase_activity
Participant: Family: GDH2 / gdh2 (NAD-GDH)
Gene:
GDH2 / gdh2 (NAD-GDH)
Family:
large NAD-specific glutamate dehydrogenases Fungal NAD-GDHs are large (about 1,100-residue) proteins unrelated in architecture to the hexameric NADP-GDHs and are placed in a separate PANTHER family.
Representative Members: GDH2 (Saccharomyces cerevisiae)UniProtKB:P33327 gdh2 (Schizosaccharomyces pombe)UniProtKB:Q9USN5

Function

L-glutamate dehydrogenase (NAD+) activityGO:0004352
Substrates: L-glutamate NAD+ H2O
Products: 2-oxoglutarate ammonium NADH

Main route releasing ammonium from glutamate; needed to supply ammonium for glutamine synthesis when glutamate is the nitrogen source. Under nitrogen catabolite repression and carbon-source control (PMID:1652057). S. cerevisiae Gdh2 is cytosolic; no location is asserted on the family role because the PomBase model places S. pombe gdh2 in mitochondria (see knowledge gap).