Carotenoid biosynthesis I — carotene backbone (GGPP -> phytoene -> lycopene -> cyclic carotenes)

The carotene backbone segment of carotenoid biosynthesis converts two molecules of the C20 isoprenoid geranylgeranyl diphosphate (GGPP) into the C40 cyclic carotenes that seed every downstream carotenoid class. Phytoene synthase performs the head-to-head condensation that commits GGPP to carotenoids, giving 15-cis-phytoene. Phytoene is then desaturated to all-trans-lycopene by one of two mutually exclusive routes: a single FAD-dependent CrtI-type desaturase in most bacteria and fungi, or the four-enzyme poly-cis route of cyanobacteria and plants (PDS, Z-ISO, ZDS, CRTISO) in which two plastoquinone-dependent desaturases each introduce two double bonds and two isomerases convert the poly-cis intermediates to the all-trans product. Lycopene cyclases then form beta rings (giving gamma- and beta-carotene) or, in plants, one epsilon ring (giving delta- and alpha-carotene). Supply of GGPP, xanthophyll formation by ring hydroxylation and epoxidation, ketolation, and oxidative cleavage to apocarotenoids (retinal, abscisic acid, strigolactones, neurosporaxanthin) are outside this module.

MODULE:carotene_backbone_biosynthesisDRAFTMetabolic Pathwaymodules/carotene_backbone_biosynthesis.yaml
carotenoid biosynthetic processGO:0016117 carotene biosynthetic processGO:0016120 beta-carotene biosynthetic processGO:1901812
GO:0016117
carotenoid biosynthetic process
GO:0016117 is the module-level process. The steps modeled here form the carotene backbone that every carotenoid biosynthetic pathway shares before branching into xanthophylls, ketocarotenoids, or apocarotenoids.
GO:0016120
carotene biosynthetic process
GO:0016120 names the hydrocarbon-carotene product class of this module. In the current ontology it descends from isoprenoid biosynthetic process via carotene metabolic process and is not a descendant of GO:0016117 carotenoid biosynthetic process, although beta-carotene biosynthetic process (GO:1901812) is; see knowledge_gaps.
KEGG:M00097
Lycopene biosynthesis, geranylgeranyl-PP => lycopene
KEGG independently defines the same GGPP-to-lycopene boundary and the same two alternative desaturation routes: phytoene synthase followed by either the single CrtI-type desaturase (K10027/K15745) or the ordered PDS, Z-ISO, ZDS, CRTISO series (K02293, K15744, K00514, K09835).
KEGG:M01045
Zeaxanthin biosynthesis, lycopene => beta-carotene => zeaxanthin
KEGG places lycopene beta-cyclase orthologs (K06443, K22502, K14605, K14606) as the lycopene-to-beta-carotene step, which is the cyclization part of this module; the subsequent hydroxylation to zeaxanthin is a xanthophyll step outside this module.
PMID:24175570
Mechanistic aspects of carotenoid biosynthesis.
Comprehensive mechanistic review covering phytoene synthase chemistry, the CrtI versus PDS/ZDS/Z-ISO/CRTISO desaturation routes, and the lycopene cyclase families used to set the boundary of this module.
PMID:25578273
Carotenoid metabolism in plants.
Plant-focused review of the plastid carotenoid pathway, including the poly-cis desaturation route, the beta/epsilon cyclase branch point, and the downstream xanthophyll and apocarotenoid branches excluded here.
PMID:15012246
GENES AND ENZYMES OF CAROTENOID BIOSYNTHESIS IN PLANTS.
Classic review that established the plant pathway enzymes and their relationship to the bacterial crt genes used as exemplars in this module.
file:modules/carotene_backbone_biosynthesis-deep-research-openscientist.md
OpenScientist carotene backbone biosynthesis module research
Module-level research supports the three-operation boundary (phytoene synthesis, four desaturations with isomerization, cyclization), the mutually exclusive but functionally interchangeable CrtI-type versus poly-cis desaturation routes (bacterial CrtI substitutes for the whole PDS/Z-ISO/ZDS/CRTISO set in planta), and at least four non-homologous cyclase families (CrtY, CrtL-type LCYB/LCYE, the fungal bifunctional synthase/cyclase, CruA/CruP). Manual assessment keeps GGPP supply, the ORANGE chaperone of PSY, the plastid terminal oxidase that re-oxidizes plastoquinone for the plant desaturases, xanthophyll formation and apocarotenoid cleavage outside the reusable core; identifiers in this module were verified against UniProt, PANTHER, Rhea, GO and the cached GO-CAM, not taken from the report.

This reusable module is taxon-neutral at the root and records lineage differences in variant sets: the desaturation route (CrtI-type versus poly-cis) and the cyclase implementation (LCYB/CrtL-type, CrtY-type, or the fungal bifunctional phytoene synthase/lycopene cyclase). Representative members orient each family without restricting the module to those organisms. Grounding: Arabidopsis PSY1 (P37271), PDS (Q07356), Z-ISO (Q9SAC0), ZDS (Q38893), CRTISO (Q9M9Y8), LCYB (Q38933) and LCYE (Q38932); cyanobacterial pds/crtP (P26294), crtQ (P74306) and crtL (Q55276); Pantoea ananatis CrtB (P21683), CrtI (P21685) and CrtY (P21687); and Neurospora crassa al-2 (P37295) and al-1 (P21334), whose activities are also captured in the production GO-CAM 62f58d8800000065 (Carotenoid biosynthesis, N. crassa). PAINT ancestral nodes are cited only where a local PTHR42923 IBD slice exists (PDS and ZDS). GGPP synthesis is covered by the isoprenoid_diphosphate_biosynthesis module; xanthophyll and apocarotenoid branches are deliberately excluded and are candidates for sibling modules.

15Nodes
9Parts
2Variant Sets
5Variants
11Annotons
6Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • carotene_backbone_biosynthesis-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

13 gene-function check(s) reflected in core functions · 0 conflict(s) · 12 evidence or coverage gap(s) (28 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
psy_activity PSY1 (Arabidopsis thaliana)
UniProtKB:P37271
Family Representative 		15-cis-phytoene synthase activity
GO:0046905 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psy_activity CrtB (Pantoea ananatis)
UniProtKB:P21683
Family Representative 		15-cis-phytoene synthase activity
GO:0046905 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psy_activity al-2 (Neurospora crassa)
UniProtKB:P37295
Family Representative 		15-cis-phytoene synthase activity
GO:0046905 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
crti_activity CrtI (Pantoea ananatis)
UniProtKB:P21685
Family Representative 		phytoene dehydrogenase activity
GO:0016166 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
crti_activity al-1 (Neurospora crassa)
UniProtKB:P21334
Family Representative 		phytoene dehydrogenase activity
GO:0016166 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pds_activity PDS (Arabidopsis thaliana)
UniProtKB:Q07356
Family Representative 		phytoene dehydrogenase activity
GO:0016166 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pds_activity pds/crtP (Synechococcus elongatus PCC 7942)
UniProtKB:P26294
Family Representative 		phytoene dehydrogenase activity
GO:0016166 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ziso_activity Z-ISO (Arabidopsis thaliana)
UniProtKB:Q9SAC0
Family Representative 		9,15,9'-tri-cis-zeta-carotene isomerase activity
GO:0090471 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
zds_activity ZDS (Arabidopsis thaliana)
UniProtKB:Q38893
Family Representative 		9,9'-di-cis-zeta-carotene desaturase activity
GO:0016719 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
zds_activity crtQ (Synechocystis sp. PCC 6803)
UniProtKB:P74306
Family Representative 		9,9'-di-cis-zeta-carotene desaturase activity
GO:0016719 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
crtiso_activity CRTISO (Arabidopsis thaliana)
UniProtKB:Q9M9Y8
Family Representative 		carotenoid isomerase activity
GO:0046608 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
crtiso_activity CRTISO / tangerine (Solanum lycopersicum)
UniProtKB:Q8S4R4
Family Representative 		carotenoid isomerase activity
GO:0046608 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
crtl_activity crtL (Synechococcus elongatus PCC 7942)
UniProtKB:Q55276
Family Representative 		lycopene beta cyclase activity
GO:0045436 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lcyb_activity LCYB / LCY1 (Arabidopsis thaliana)
UniProtKB:Q38933
Family Representative 		lycopene beta cyclase activity
GO:0045436 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
crty_activity CrtY (Pantoea ananatis)
UniProtKB:P21687
Family Representative 		lycopene beta cyclase activity
GO:0045436 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
al2_cyclase_activity al-2 (Neurospora crassa)
UniProtKB:P37295
Family Representative 		lycopene beta cyclase activity
GO:0045436 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
lcye_activity LCYE / LUT2 (Arabidopsis thaliana)
UniProtKB:Q38932
Family Representative 		lycopene epsilon cyclase activity
GO:0045435 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psy_activity Phytoene synthase (PSY/CrtB) family
PANTHER:PTHR31480
Family 		15-cis-phytoene synthase activity
GO:0046905 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31480.
crti_activity CrtI-type phytoene desaturase family
PANTHER:PTHR43734
Family 		phytoene dehydrogenase activity
GO:0016166 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR43734.
pds_activity PDS/CrtP 15-cis-phytoene desaturase family
PANTHER:PTHR42923:SF45
Family 		phytoene dehydrogenase activity
GO:0016166 		Family Supported
Family review supports GO:0016166 for PANTHER:PTHR42923:SF45. PDS (SF45), as carotene_backbone_biosynthesis selects.
ziso_activity Z-ISO 15-cis-zeta-carotene isomerase family
PANTHER:PTHR35988:SF2
Family 		9,15,9'-tri-cis-zeta-carotene isomerase activity
GO:0090471 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR35988:SF2.
zds_activity ZDS/CrtQ zeta-carotene desaturase family
PANTHER:PTHR42923:SF41
Family 		9,9'-di-cis-zeta-carotene desaturase activity
GO:0016719 		Family Supported
Family review supports GO:0016719 for PANTHER:PTHR42923:SF41. ZDS (SF41), as carotene_backbone_biosynthesis selects.
crtiso_activity CRTISO/CrtH prolycopene isomerase family
PANTHER:PTHR46313:SF3
Family 		carotenoid isomerase activity
GO:0046608 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR46313:SF3.
crtl_activity CrtL-type lycopene beta-cyclase subfamily
PANTHER:PTHR39757:SF5
Family 		lycopene beta cyclase activity
GO:0045436 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR39757:SF5.
lcyb_activity Plant LCYB lycopene beta-cyclase subfamily
PANTHER:PTHR43876:SF15
Family 		lycopene beta cyclase activity
GO:0045436 		Family Supported
Family review supports GO:0045436 for PANTHER:PTHR43876:SF15. Plant LCYB (SF15), as carotene_backbone_biosynthesis selects. PANTHER classification files place Arabidopsis LCYB here, while UniProt cross-references it to another family.
crty_activity CrtY-type lycopene beta-cyclase family
Family 		lycopene beta cyclase activity
GO:0045436 		Family Id Missing
The family has no identifier linking it to a curated family review.
al2_cyclase_activity Bifunctional lycopene cyclase/phytoene synthase family (cyclase domain)
PANTHER:PTHR31480
Family 		lycopene beta cyclase activity
GO:0045436 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31480.
lcye_activity LCYE lycopene epsilon-cyclase family
PANTHER:PTHR39757:SF3
Family 		lycopene epsilon cyclase activity
GO:0045435 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR39757:SF3.

Gene-review completeness (12/16 grounded genes reviewed)

12 complete review(s) · 12 with deep research · 4 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
al-1 P21334 ✓ ✓ ✓
al-2 P37295 ✓ ✓ ✓
crtB P21683 ✓ ✓ ✓
crtI P21685 ✓ ✓ ✓
CRTISO Q9M9Y8 ✓ ✓ ✓
crtY P21687 ✓ ✓ ✓
LCYB Q38933 ✓ ✓ ✓
LCYE Q38932 ✓ ✓ ✓
pds/crtP (Synechococcus elongatus PCC 7942) P26294 ✗ — —
crtQ (Synechocystis sp. PCC 6803) P74306 ✗ — —
PDS Q07356 ✓ ✓ ✓
PSY P37271 ✓ ✓ ✓
crtL (Synechococcus elongatus PCC 7942) Q55276 ✗ — —
CRTISO / tangerine (Solanum lycopersicum) Q8S4R4 ✗ — —
Z-ISO Q9SAC0 ✓ ✓ ✓
ZDS Q38893 ✓ ✓ ✓

Details

Context
membraneGO:0016020
Carotene backbone biosynthesis (GGPP -> phytoene -> lycopene -> cyclic carotenes)Metabolic Pathwaycarotene_backbone_biosynthesis
carotenoid biosynthetic processGO:0016117 carotene biosynthetic processGO:0016120 beta-carotene biosynthetic processGO:1901812
Context
membraneGO:0016020

Connections

Phytoene synthase supplies 15-cis-phytoene to the desaturation step.
The desaturation route supplies all-trans-lycopene to the cyclases.
Part 1: Phytoene synthesis (commitment of GGPP to carotenoids)
Phytoene synthase step (2 GGPP -> 15-cis-phytoene)Reactionphytoene_synthesis

Phytoene synthase condenses two GGPP molecules head-to-head via prephytoene diphosphate to 15-cis-phytoene, the first C40 carotenoid and the committed step of the pathway.

Annotons

15-cis-phytoene synthase activity
psy_activity
Participant: Family: Phytoene synthase (PSY/CrtB) family
Family:
Phytoene synthase (PSY/CrtB) familyPANTHER:PTHR31480 The official family name reflects the fungal bifunctional members; plant PSY and bacterial CrtB are single-domain phytoene synthases in the same family. UniProt assigns the exemplars to the family without a subfamily, so the family id is used.
Representative Members: PSY1 (Arabidopsis thaliana)UniProtKB:P37271 CrtB (Pantoea ananatis)UniProtKB:P21683 al-2 (Neurospora crassa)UniProtKB:P37295
Required Function:
15-cis-phytoene synthase activityGO:0046905

Function

15-cis-phytoene synthase activityGO:0046905
Substrates: (2E,6E,10E)-geranylgeranyl diphosphate
Products: 15-cis-phytoene diphosphate

Processes

phytoene biosynthetic processGO:1901174

Commits GGPP to the carotenoid pathway by forming the first C40 carotene, 15-cis-phytoene.

Part 2: Desaturation and isomerization of phytoene to all-trans-lycopene
Phytoene -> all-trans-lycopene (four desaturations)Metabolic Pathwayphytoene_desaturation_to_lycopene

Four double bonds are introduced into 15-cis-phytoene to give all-trans-lycopene. Bacteria and fungi use one FAD-dependent CrtI-type desaturase that also isomerizes the 15-cis bond; plants and cyanobacteria use two plastoquinone-dependent desaturases (PDS, ZDS) that each introduce two cis double bonds, and two isomerases (Z-ISO, CRTISO) that convert the poly-cis intermediates to the all-trans configuration.

lycopene biosynthetic processGO:1901177
Variant set: Phytoene desaturation route by desaturase enzyme system (Exactly One)

The two routes are mutually exclusive within a lineage: CrtI-type desaturases are found in most non-photosynthetic bacteria and in fungi, while the poly-cis route is found in cyanobacteria, algae and plants. Both are recognized by KEGG M00097.

CrtI-type single-enzyme desaturationReactioncrti_type_desaturation

A single FAD-dependent desaturase of the amine-oxidase fold carries out all four desaturations and the 15-cis to trans isomerization, converting 15-cis-phytoene to all-trans-lycopene via phytofluene, zeta-carotene and neurosporene. Fungal orthologs (al-1 type) add a fifth desaturation to 3,4-didehydrolycopene, feeding the torulene branch, which is outside this module.

Context
bacteriaNCBITaxon:2 fungiNCBITaxon:4751

Annotons

Lycopene-forming phytoene desaturase activity
crti_activity
Participant: Family: CrtI-type phytoene desaturase family
Family:
CrtI-type phytoene desaturase familyPANTHER:PTHR43734 Family-level id is used because PANTHER splits the reviewed exemplars across subfamilies (Pantoea CrtI in SF3, whose official label is a ketolase name, and Neurospora al-1 in SF1). The lycopene-forming activity is imposed by the required function and Rhea, not by the PANTHER label.
Representative Members: CrtI (Pantoea ananatis)UniProtKB:P21685 al-1 (Neurospora crassa)UniProtKB:P21334
Required Function:
phytoene dehydrogenase activityGO:0016166

Function

phytoene dehydrogenase activityGO:0016166
Substrates: 15-cis-phytoene electron acceptor
Products: all-trans-lycopene reduced electron acceptor
Cofactors: FAD

Performs all four desaturations from phytoene to all-trans-lycopene as a single enzyme.

Poly-cis desaturation/isomerization route (PDS, Z-ISO, ZDS, CRTISO)Metabolic Pathwaypoly_cis_desaturation_isomerization

Two plastoquinone-dependent desaturases each introduce two cis double bonds, and two isomerases restore the all-trans configuration: PDS converts 15-cis-phytoene to 9,15,9'-tri-cis-zeta-carotene; Z-ISO isomerizes the 15-cis bond to give 9,9'-di-cis-zeta-carotene; ZDS forms 7,7',9,9'-tetra-cis-lycopene (prolycopene); CRTISO isomerizes prolycopene to all-trans-lycopene. Light-driven photoisomerization can partially substitute for the two isomerases in illuminated tissue, but the enzymes are required in the dark and in non-photosynthetic tissues.

Context
cyanobacteriaNCBITaxon:1117 green plantsNCBITaxon:33090

The taxon context lists the lineages grounded by the exemplars used here. Plant-type CrtP/CrtQ desaturases are also reported in some anoxygenic green sulfur bacteria, apparently without a Z-ISO ortholog, so the route is not strictly confined to oxygenic phototrophs; no exemplar from those lineages was verified in this session.

Connections

pds_step -> ziso_step Provides Input For
PDS supplies tri-cis-zeta-carotene to Z-ISO.
ziso_step -> zds_step Provides Input For
Z-ISO supplies di-cis-zeta-carotene to ZDS.
zds_step -> crtiso_step Provides Input For
ZDS supplies prolycopene to CRTISO.
Part 1: Phytoene desaturation to tri-cis-zeta-carotene
PDS step (15-cis-phytoene -> 9,15,9'-tri-cis-zeta-carotene)Reactionpds_step

Annotons

15-cis-phytoene desaturase activity
pds_activity
Participant: Family: PDS/CrtP 15-cis-phytoene desaturase family
Family:
PDS/CrtP 15-cis-phytoene desaturase familyPANTHER:PTHR42923:SF45 The official label is plant-biased; the subfamily also holds the cyanobacterial pds/crtP exemplar. The label is retained verbatim without asserting localization.
Representative Members: PDS (Arabidopsis thaliana)UniProtKB:Q07356 pds/crtP (Synechococcus elongatus PCC 7942)UniProtKB:P26294
Required Function:
phytoene dehydrogenase activityGO:0016166

Function

phytoene dehydrogenase activityGO:0016166
Substrates: 15-cis-phytoene plastoquinone
Products: 9,15,9'-tri-cis-zeta-carotene plastoquinol

Introduces the first two double bonds, producing the tri-cis-zeta-carotene intermediate.

Part 2: 15-cis isomerization of tri-cis-zeta-carotene
Z-ISO step (9,15,9'-tri-cis- -> 9,9'-di-cis-zeta-carotene)Reactionziso_step

Annotons

15-cis-zeta-carotene isomerase activity
ziso_activity
Participant: Family: Z-ISO 15-cis-zeta-carotene isomerase family
Family:
Z-ISO 15-cis-zeta-carotene isomerase familyPANTHER:PTHR35988:SF2
Representative Members: Z-ISO (Arabidopsis thaliana)UniProtKB:Q9SAC0
Required Function:
9,15,9'-tri-cis-zeta-carotene isomerase activityGO:0090471

Function

9,15,9'-tri-cis-zeta-carotene isomerase activityGO:0090471
Substrates: 9,15,9'-tri-cis-zeta-carotene
Products: 9,9'-di-cis-zeta-carotene

Isomerizes the central 15-cis bond so that ZDS can act; light can partially substitute for this step.

Part 3: Zeta-carotene desaturation to prolycopene
ZDS step (9,9'-di-cis-zeta-carotene -> 7,7',9,9'-tetra-cis-lycopene)Reactionzds_step

Annotons

Zeta-carotene desaturase activity
zds_activity
Participant: Family: ZDS/CrtQ zeta-carotene desaturase family
Family:
ZDS/CrtQ zeta-carotene desaturase familyPANTHER:PTHR42923:SF41 The official label is plant-biased; the subfamily also holds the cyanobacterial crtQ exemplar. The label is retained verbatim without asserting localization.
Representative Members: ZDS (Arabidopsis thaliana)UniProtKB:Q38893 crtQ (Synechocystis sp. PCC 6803)UniProtKB:P74306
Required Function:
9,9'-di-cis-zeta-carotene desaturase activityGO:0016719

Function

9,9'-di-cis-zeta-carotene desaturase activityGO:0016719
Substrates: 9,9'-di-cis-zeta-carotene plastoquinone
Products: 7,7',9,9'-tetra-cis-lycopene plastoquinol

Introduces the third and fourth double bonds, producing prolycopene.

Part 4: Prolycopene isomerization to all-trans-lycopene
CRTISO step (7,7',9,9'-tetra-cis-lycopene -> all-trans-lycopene)Reactioncrtiso_step

Annotons

Prolycopene isomerase activity
crtiso_activity
Participant: Family: CRTISO/CrtH prolycopene isomerase family
Family:
CRTISO/CrtH prolycopene isomerase familyPANTHER:PTHR46313:SF3
Representative Members: CRTISO (Arabidopsis thaliana)UniProtKB:Q9M9Y8 CRTISO / tangerine (Solanum lycopersicum)UniProtKB:Q8S4R4
Required Function:
carotenoid isomerase activityGO:0046608

Function

carotenoid isomerase activityGO:0046608
Substrates: 7,7',9,9'-tetra-cis-lycopene
Products: all-trans-lycopene

Converts prolycopene to the all-trans-lycopene substrate of the cyclases; light can partially substitute for this step.

Part 3: Cyclization of lycopene to cyclic carotenes
Lycopene cyclization (lycopene -> beta-carotene or alpha-carotene)Metabolic Pathwaylycopene_cyclization

Lycopene cyclases fold the psi end groups of all-trans-lycopene into six-membered rings. Two beta-ring cyclizations give gamma-carotene then beta-carotene. In plants an epsilon cyclase forms one epsilon ring (delta-carotene), and a beta cyclase then forms the other ring to give alpha-carotene; the beta and epsilon branches are the branch point between the beta,beta- and beta,epsilon-xanthophyll series.

beta-carotene biosynthetic processGO:1901812 alpha-carotene biosynthetic processGO:1901824

Connections

In the alpha-carotene branch the epsilon cyclase acts first and a beta cyclase completes the second ring.
Part 1: Beta-ring cyclization
Beta cyclization (lycopene -> gamma-carotene -> beta-carotene)Reactionbeta_ring_cyclization

Beta-ring formation at one or both psi ends of lycopene. Three non-homologous or distantly related implementations exist; the required function is the same.

Variant set: Lycopene beta-cyclase implementation by enzyme family (One Or More)
LCYB/CrtL-type lycopene beta-cyclaseReactionlcyb_crtl_type_beta_cyclase

Homologous plant LCYB and cyanobacterial CrtL beta cyclases (FAD-dependent, related to LCYE). PANTHER's HMM classification splits the reviewed exemplars across two families, so two family descriptors carry the same role here; either satisfies the variant.

Context
cyanobacteriaNCBITaxon:1117 green plantsNCBITaxon:33090

Annotons

CrtL-type lycopene beta cyclase activity
crtl_activity
Participant: Family: CrtL-type lycopene beta-cyclase subfamily
Family:
CrtL-type lycopene beta-cyclase subfamilyPANTHER:PTHR39757:SF5 The official subfamily label is an uninformative rice locus name and the parent family PTHR39757 is unnamed in PANTHER. Membership of the reviewed cyanobacterial crtL exemplar (and UniProt's cross-reference of Arabidopsis LCYB to this subfamily) identifies it as a lycopene beta-cyclase subfamily, sister to the LCYE subfamily SF3.
Representative Members: crtL (Synechococcus elongatus PCC 7942)UniProtKB:Q55276
Required Function:
lycopene beta cyclase activityGO:0045436

Function

lycopene beta cyclase activityGO:0045436
Substrates: all-trans-lycopene
Products: gamma-carotene all-trans-beta-carotene

Forms beta rings at the psi ends of lycopene.

Plant LCYB lycopene beta cyclase activity
lcyb_activity
Participant: Family: Plant LCYB lycopene beta-cyclase subfamily
Family:
Plant LCYB lycopene beta-cyclase subfamilyPANTHER:PTHR43876:SF15 PANTHER's per-organism classification places the reviewed Arabidopsis LCYB in this subfamily of a family whose official name is taken from the COQ6 monooxygenase; UniProt instead cross-references the same protein to PTHR39757:SF5. The subfamily is used because it is where PANTHER's own classification puts the exemplar; see knowledge_gaps.
Representative Members: LCYB / LCY1 (Arabidopsis thaliana)UniProtKB:Q38933
Required Function:
lycopene beta cyclase activityGO:0045436

Function

lycopene beta cyclase activityGO:0045436
Substrates: all-trans-lycopene
Products: gamma-carotene all-trans-beta-carotene

Forms beta rings at the psi ends of lycopene and of delta-carotene in the alpha-carotene branch.

CrtY-type lycopene beta-cyclaseReactioncrty_type_beta_cyclase
Context
bacteriaNCBITaxon:2

Annotons

CrtY lycopene beta cyclase activity
crty_activity
Participant: Family: CrtY-type lycopene beta-cyclase family
Family:
CrtY-type lycopene beta-cyclase family No PANTHER family is assigned to the reviewed Pantoea CrtY exemplar in UniProt, so no family id is asserted; the descriptor is grounded by its representative member and required function.
Representative Members: CrtY (Pantoea ananatis)UniProtKB:P21687
Required Function:
lycopene beta cyclase activityGO:0045436

Function

lycopene beta cyclase activityGO:0045436
Substrates: all-trans-lycopene
Products: gamma-carotene all-trans-beta-carotene

Bacterial beta-cyclase of the crt gene cluster, forming gamma- then beta-carotene.

Bifunctional phytoene synthase/lycopene cyclase (fungal)Reactionbifunctional_psy_cyclase_beta_cyclase
Context
fungiNCBITaxon:4751

Annotons

Bifunctional al-2 lycopene beta cyclase activity
al2_cyclase_activity
Participant: Family: Bifunctional lycopene cyclase/phytoene synthase family (cyclase domain)
Family:
Bifunctional lycopene cyclase/phytoene synthase family (cyclase domain)PANTHER:PTHR31480 The fungal members carry an N-terminal lycopene cyclase domain fused to the phytoene synthase domain; the same protein appears in phytoene_synthesis for its synthase activity.
Representative Members: al-2 (Neurospora crassa)UniProtKB:P37295
Required Function:
lycopene beta cyclase activityGO:0045436

Function

lycopene beta cyclase activityGO:0045436
Substrates: all-trans-lycopene
Products: gamma-carotene all-trans-beta-carotene

Cyclase domain of the fungal bifunctional enzyme; forms gamma- and beta-carotene and, from 3,4-didehydrolycopene, torulene (outside this module).

Part 2: Epsilon-ring cyclization (alpha-carotene branch) (optional)
Epsilon cyclization (lycopene -> delta-carotene)Reactionepsilon_ring_cyclization

Plant lycopene epsilon cyclase forms a single epsilon ring at one psi end of lycopene, giving delta-carotene; a beta cyclase then completes alpha-carotene. This branch is optional because many carotenogenic bacteria and fungi make only beta,beta carotenes.

Context
green plantsNCBITaxon:33090

Annotons

Lycopene epsilon cyclase activity
lcye_activity
Participant: Family: LCYE lycopene epsilon-cyclase family
Family:
LCYE lycopene epsilon-cyclase familyPANTHER:PTHR39757:SF3
Representative Members: LCYE / LUT2 (Arabidopsis thaliana)UniProtKB:Q38932
Required Function:
lycopene epsilon cyclase activityGO:0045435

Function

lycopene epsilon cyclase activityGO:0045435
Substrates: all-trans-lycopene
Products: delta-carotene

Processes

alpha-carotene biosynthetic processGO:1901824

Forms the single epsilon ring that commits lycopene to the alpha-carotene (beta,epsilon) branch.