Carnitine acyltransferase shuttle (mitochondrial import of acyl and acetyl units)

The carnitine shuttle moves activated acyl groups across membranes that are impermeable to acyl-CoA. A carnitine acyltransferase on the donor side transfers the acyl group from CoA to L-carnitine; the resulting acylcarnitine is carried across the mitochondrial inner membrane by a mitochondrial-carrier-family carnitine/acylcarnitine translocase in exchange for free carnitine; and a matrix carnitine acyltransferase reverses the transfer, regenerating acyl-CoA and releasing carnitine for recycling. The same chemistry serves different cargo in different lineages. In animals the shuttle imports long-chain fatty acids for mitochondrial beta-oxidation: carnitine palmitoyltransferase 1 on the outer membrane catalyses the committed, malonyl-CoA-inhibited step and carnitine palmitoyltransferase 2 on the matrix side of the inner membrane regenerates long-chain acyl-CoA. In fungi such as budding yeast, where beta-oxidation is peroxisomal, the shuttle carries acetyl units: carnitine acetyltransferases in the peroxisome, cytosol and at the mitochondrial outer membrane form acetylcarnitine from acetyl-CoA produced by beta-oxidation or by cytosolic acetate and ethanol metabolism, and the mitochondrial isoform regenerates acetyl-CoA in the matrix for the tricarboxylic acid cycle. Cells take up carnitine through a plasma-membrane transporter; budding yeast cannot make carnitine and depends on uptake. Inherited defects of the animal components (SLC22A5, CPT1A, SLC25A20, CPT2) cause fatty-acid-oxidation disorders.

MODULE:carnitine_shuttleDRAFTMetabolic Pathwaymodules/carnitine_shuttle.yaml
carnitine shuttleGO:0006853
YeastPathways:PWY3O-4
carnitine shuttle (S. cerevisiae, SGD YeastPathways)
YeastCyc lists CARNITINE-O-ACETYLTRANSFERASE-RXN (CAT2, YAT1, YAT2) and the reverse matrix reaction RXN3O-37 (CAT2). The pathway comment names Crc1p as the translocase, but CRC1 is not attached to any reaction; it and the plasma-membrane carnitine transporter AGP2 were added.
GO:0006853
carnitine shuttle
Module-level process for carnitine-dependent acyl transfer across mitochondrial membranes.
Reactome:R-HSA-200425
Carnitine shuttle
Step order and reaction directions of the long-chain branch follow the human Reactome "Carnitine shuttle" pathway (R-HSA-200425): R-HSA-165026 (SLC22A5 uptake), R-HSA-200406 (CPT1A), R-HSA-200424 (SLC25A20 antiport) and R-HSA-200410 (CPT2).
PMID:20889721
Intracellular acetyl unit transport in fungal carbon metabolism.
In fungi, carnitine acetyltransferases exchange the CoA of acetyl-CoA for carnitine so that acetylcarnitine can move between compartments; a citrate synthase-dependent route is the alternative.
PMID:10545096
Molecular characterization of carnitine-dependent transport of acetyl-CoA from peroxisomes to mitochondria in Saccharomyces cerevisiae and identification of a plasma membrane carnitine transporter, Agp2p.
Carnitine-dependent transport of peroxisomal acetyl-CoA to mitochondria requires CAT2, the translocase YOR100C/CRC1 and the plasma-membrane carnitine transporter AGP2.
PMID:10622748
Identification of the mitochondrial carnitine carrier in Saccharomyces cerevisiae.
Reconstituted Crc1p transports carnitine, acetylcarnitine and propionylcarnitine, and much less medium- and long-chain acylcarnitines.
PMID:7628448
Peroxisomal and mitochondrial carnitine acetyltransferases of Saccharomyces cerevisiae are encoded by a single gene.
One gene (YCAT/CAT2) encodes both the mitochondrial and the peroxisomal carnitine acetyltransferase, via alternative transcript starts.
PMID:7628449
The membrane of peroxisomes in Saccharomyces cerevisiae is impermeable to NAD(H) and acetyl-CoA under in vivo conditions.
The peroxisomal membrane is impermeable to acetyl-CoA in vivo; acetyl units leave via carnitine acetyltransferase or the citrate synthase route.
PMID:11329169
Carnitine-dependent metabolic activities in Saccharomyces cerevisiae: three carnitine acetyltransferases are essential in a carnitine-dependent strain.
CAT2 (peroxisomal and mitochondrial), YAT1 (presumably outer mitochondrial membrane) and YAT2 are all essential for growth on non-fermentable carbon sources in a cit2 strain.
PMID:8262985
The ethanol-inducible YAT1 gene from yeast encodes a presumptive mitochondrial outer carnitine acetyltransferase.
YAT1 is ethanol/acetate-induced and binds mitochondria in a protease-sensitive location, consistent with an outer-membrane carnitine acetyltransferase.
PMID:18427809
Carnitine and carnitine acetyltransferases in the yeast Saccharomyces cerevisiae: a role for carnitine in stress protection.
Overexpression of single CAT genes does not cross-complement, suggesting specific roles for each enzyme.
PMID:27143389
Requirements for Carnitine Shuttle-Mediated Translocation of Mitochondrial Acetyl Moieties to the Yeast Cytosol.
Fatty-acid-grown yeast uses the shuttle to import acetyl units into mitochondria; export to the cytosol does not normally occur in vivo but can be enabled by mutations including in YAT2.
file:yeast/CAT2/CAT2-ai-review.yaml
CAT2 gene review (S. cerevisiae)
Core function GO:0004092 carnitine O-acetyltransferase activity in mitochondria and peroxisomes.
file:human/SLC22A5/SLC22A5-ai-review.yaml
SLC22A5 gene review (human)
The plasma-membrane carnitine-uptake step (UniProtKB:O76082, GO:0015226) matches the completed human SLC22A5/OCTN2 review.
file:human/CPT1A/CPT1A-ai-review.yaml
CPT1A gene review (human)
The CPT1 step grounding (UniProtKB:P50416, GO:0004095, mitochondrial outer membrane) matches the completed human CPT1A review.
file:human/SLC25A20/SLC25A20-ai-review.yaml
SLC25A20 gene review (human)
The translocase step (UniProtKB:O43772, GO:0015227, inner membrane) matches the completed human SLC25A20 review.
file:human/CPT2/CPT2-ai-review.yaml
CPT2 gene review (human)
The CPT2 step grounding (UniProtKB:P23786, GO:0004095, inner membrane) matches the completed human CPT2 review.
11Nodes
4Parts
3Variant Sets
6Variants
7Annotons
4Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:carnitine_shuttle 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.

Function consistency and core coverage

8 gene-function check(s) reflected in core functions · 0 conflict(s) · 3 evidence or coverage gap(s) (15 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
slc22a5_activity SLC22A5 / OCTN2 (human)
UniProtKB:O76082
Family Representative 		carnitine transmembrane transporter activity
GO:0015226 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cpt1a_activity CPT1A (human, liver isoform)
UniProtKB:P50416
Family Representative 		carnitine O-palmitoyltransferase activity
GO:0004095 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cat_acetyl_donor_activity CAT2 (Saccharomyces cerevisiae; peroxisomal isoform)
UniProtKB:P32796
Family Representative 		carnitine O-acetyltransferase activity
GO:0004092 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cat_acetyl_donor_activity YAT1 (Saccharomyces cerevisiae; mitochondrial outer membrane)
UniProtKB:P80235
Family Representative 		carnitine O-acetyltransferase activity
GO:0004092 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cat_acetyl_donor_activity YAT2 (Saccharomyces cerevisiae; cytosolic)
UniProtKB:P40017
Family Representative 		carnitine O-acetyltransferase activity
GO:0004092 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
slc25a20_activity SLC25A20 / CACT (human)
UniProtKB:O43772
Family Representative 		O-acyl-L-carnitine transmembrane transporter activity
GO:0015227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
slc25a20_activity CRC1 (Saccharomyces cerevisiae)
UniProtKB:Q12289
Family Representative 		O-acyl-L-carnitine transmembrane transporter activity
GO:0015227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cpt2_activity CPT2 (human)
UniProtKB:P23786
Family Representative 		carnitine O-palmitoyltransferase activity
GO:0004095 		Annotation Supported
A retained annotation or curated replacement supports this function, but core_functions does not yet reflect it.
cat2_mito_activity CAT2 (Saccharomyces cerevisiae; mitochondrial isoform)
UniProtKB:P32796
Family Representative 		carnitine O-acetyltransferase activity
GO:0004092 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
slc22a5_activity OCTN2/SLC22A5 carnitine transporter subfamily
PANTHER:PTHR24064:SF283
Family 		carnitine transmembrane transporter activity
GO:0015226 		Family Supported
Family review supports GO:0015226 for PANTHER:PTHR24064:SF283. Safe for the vertebrate OCTN clade (PTN007768016: SF283 SLC22A5, SF222 SLC22A4, SF680 Slc22a21) and for SLC22A16 (SF186, separately asserted at PTN002782663). Not safe for the family: PHO84, GIT1, PHT1 and the OCT/OAT subfamilies do not carry it. The SLC22A5 uptake step in the carnitine shuttle module is therefore grounded on PTHR24064:SF283 rather than the whole family.
cpt1a_activity CPT1A carnitine O-palmitoyltransferase subfamily
PANTHER:PTHR22589:SF74
Family 		carnitine O-palmitoyltransferase activity
GO:0004095 		Family Supported
Family review supports GO:0004095 for PANTHER:PTHR22589:SF74. CPT1A, CPT1B and CPT2 lineages only (PAINT nodes PTN001097100 and PTN000501944). Not yeast CAT2/YAT1/YAT2, not CRAT/CROT, not ChAT, and pruned from CPT1C. The CPT1A and CPT2 annotons in the carnitine shuttle module are therefore grounded on their respective subfamilies rather than on the whole family.
cat_acetyl_donor_activity Carnitine O-acyltransferase family (acetyltransferase members)
Family 		carnitine O-acetyltransferase activity
GO:0004092 		Family Id Missing
The family has no identifier linking it to a curated family review.
slc25a20_activity Mitochondrial carnitine/acylcarnitine carrier family (SLC25A20, CRC1)
Family 		O-acyl-L-carnitine transmembrane transporter activity
GO:0015227 		Family Id Missing
The family has no identifier linking it to a curated family review.
cpt2_activity CPT2 carnitine O-palmitoyltransferase subfamily
PANTHER:PTHR22589:SF51
Family 		carnitine O-palmitoyltransferase activity
GO:0004095 		Family Supported
Family review supports GO:0004095 for PANTHER:PTHR22589:SF51. CPT1A, CPT1B and CPT2 lineages only (PAINT nodes PTN001097100 and PTN000501944). Not yeast CAT2/YAT1/YAT2, not CRAT/CROT, not ChAT, and pruned from CPT1C. The CPT1A and CPT2 annotons in the carnitine shuttle module are therefore grounded on their respective subfamilies rather than on the whole family.
cat2_mito_activity CAT2 mitochondrial/peroxisomal carnitine O-acetyltransferase subfamily
PANTHER:PTHR22589:SF103
Family 		carnitine O-acetyltransferase activity
GO:0004092 		Family Supported
Family review supports GO:0004092 for PANTHER:PTHR22589:SF103. Short-chain carnitine acetyltransferases: yeast CAT2 (SF103, PTN001097241), YAT1 (SF29) and YAT2 (SF48) (both under PTN001097079), and animal CRAT (SF50, PTN000502168). Not the CPT subfamilies, CROT or ChAT. The combined CAT2/YAT1/YAT2 annoton in the carnitine shuttle module omits a single machine-readable family id because its representatives span SF103, SF29 and SF48.

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

6 complete review(s) · 6 with deep research · 0 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
AGP2 P38090 ✓ ✓ ✓
CAT2 P32796 ✓ ✓ ✓
CPT1A P50416 ✓ 47/53 ✗
CPT2 P23786 ✓ ✓ ✓
CRC1 Q12289 ✓ ✓ ✓
SLC22A5 O76082 ✓ 87/89 ✗
SLC25A20 O43772 ✓ ✓ ✗
YAT1 P80235 ✓ 16/17 ✓
YAT2 P40017 ✓ ✓ ✓

Details

Context
EukaryotaNCBITaxon:2759
Carnitine acyltransferase shuttleMetabolic Pathwaycarnitine_shuttle
carnitine shuttleGO:0006853
Context
EukaryotaNCBITaxon:2759

GENERALIZE (YeastPathways project, 2026-10): the former human long-chain shuttle was broadened to carnitine acyltransferase shuttles with the same chemistry but different cargo. The two transferase steps became ONE_OR_MORE variant sets on the axis "acyl cargo": CPT1/CPT2 (GO:0004095, long-chain, animals) vs carnitine acetyltransferases (GO:0004092, acetyl, fungi). All transferases are in PTHR22589. The donor-side acetyl variant groups the three S. cerevisiae paralogs (peroxisomal CAT2 isoform, YAT1 at the mitochondrial outer membrane, cytosolic YAT2) without a single location; the matrix variant is the mitochondrial CAT2 isoform (one gene, two targeted forms; PMID:7628448). The translocase step gained CRC1 (same PANTHER family PTHR45624 as SLC25A20; short-chain preference, PMID:10622748). Carnitine uptake became an EXACTLY_ONE variant set with SLC22A5 (animals) and AGP2 (budding yeast, PMID:10545096). Module-level compartment context was replaced by annoton locations because the donor compartment differs by cargo (mitochondrial outer membrane, peroxisome, cytosol). In yeast the shuttle is in vivo effectively unidirectional (import of acetyl units into mitochondria; PMID:27143389), and it is redundant with the peroxisomal citrate synthase/glyoxylate route (PMID:7628449, PMID:11329169). YeastCyc corrections: PWY3O-4 names Crc1p in its comment but attaches it to no reaction, and AGP2 is absent. GO-CAM disagreements: YeastPathways_PWY3O-4 places CAT2, YAT1 and YAT2 in cytosol (CAT2 is peroxisomal/mitochondrial, YAT1 mitochondrial outer membrane), gives no location for the matrix reaction and lacks the translocase. The medium-chain/peroxisomal mammalian acyltransferases CRAT and CROT are not modelled. Downstream, long-chain acyl-CoA enters mitochondrial beta-oxidation (fatty_acid_beta_oxidation) and acetyl-CoA enters the TCA cycle (tca_cycle).

Connections

slc22a5_step -> cpt1_step Provides Input For
Imported L-carnitine is the acyl acceptor of the donor-side acyltransferase.
cpt1_step -> slc25a20_step Provides Input For
Acylcarnitine (or acetylcarnitine) is imported into the matrix by the translocase.
slc25a20_step -> cpt2_step Provides Input For
Matrix acylcarnitine is converted back to acyl-CoA.
cpt2_step -> slc25a20_step Provides Input For
Free carnitine released in the matrix is exported by the translocase (the antiport counter-substrate), recycling carnitine and closing the shuttle.
Part 1: cellular carnitine uptake (supplies the carnitine pool)
L-carnitine import across the plasma membraneTransport Stepslc22a5_step
Variant set: Plasma-membrane carnitine transporter by transporter family (lineage) (Exactly One)
Na+-dependent OCTN carnitine transporter (animals)Transport Stepoctn2_uptake_variant

Annotons

SLC22A5/OCTN2: Na+-dependent carnitine transporter
slc22a5_activity
Participant: Family: OCTN2/SLC22A5 carnitine transporter subfamily
Family:
OCTN2/SLC22A5 carnitine transporter subfamilyPANTHER:PTHR24064:SF283
Representative Members: SLC22A5 / OCTN2 (human)UniProtKB:O76082

Function

carnitine transmembrane transporter activityGO:0015226
Substrates: L-carnitine (extracellular) sodium ion (cotransported)
Products: L-carnitine (cytosol)

Locations

plasma membraneGO:0005886

High-affinity, sodium-dependent plasma-membrane carnitine importer; also mediates renal carnitine reabsorption. Deficiency causes primary (systemic) carnitine deficiency.

AGP2-dependent carnitine uptake (budding yeast)Transport Stepagp2_uptake_variant

Annotons

AGP2: plasma-membrane carnitine uptake regulator
agp2_activity
Participant: Family: AGP2-type amino acid permease-family carnitine uptake regulator
Family:
AGP2-type amino acid permease-family carnitine uptake regulator No PANTHER id: AGP2 is in the broad amino acid permease family PTHR43341, whose members are mostly not carnitine transporters.
Representative Members: AGP2 (Saccharomyces cerevisiae)UniProtKB:P38090

Locations

plasma membraneGO:0005886

Required for efficient carnitine uptake in yeast, which cannot synthesise carnitine.

PMID:23755272
Agp2 is proposed to regulate expression of other carnitine and polyamine permeases rather than transport them itself.
we also demonstrate for the first time that in cells lacking a functional AGP2 gene nearly 172 genes are downregulated as compared to the parent

Disputed activity. No direct transporter activity is asserted here: the AGP2 gene review asserts no molecular function; GOA has only IMP "positive regulation of carnitine transmembrane transport"; and Aouida et al. 2013 (PMID:23755272, full text) show that Agp2 sustains expression of the HNM1, DUR3 and SAM3 permeases and propose it acts mainly as a regulator or transceptor. HNM1 carries much of the carnitine uptake.

Part 2: acyl transfer from CoA to carnitine (donor side)
acyl-CoA + L-carnitine to acylcarnitine + CoAReactioncpt1_step
Variant set: Donor-side carnitine acyltransferase by cargo by acyl cargo (long-chain acyl vs acetyl) / lineage (One Or More)
CPT1 long-chain acyl transfer at the mitochondrial outer membrane (animals)Reactioncpt1_long_chain_variant

Annotons

CPT1A: carnitine palmitoyltransferase 1 (liver)
cpt1a_activity
Participant: Family: CPT1A carnitine O-palmitoyltransferase subfamily
Family:
CPT1A carnitine O-palmitoyltransferase subfamilyPANTHER:PTHR22589:SF74
Representative Members: CPT1A (human, liver isoform)UniProtKB:P50416

Function

carnitine O-palmitoyltransferase activityGO:0004095
Substrates: long-chain acyl-CoA L-carnitine
Products: long-chain O-acylcarnitine coenzyme A

Locations

mitochondrial outer membraneGO:0005741

Committed, rate-limiting step of long-chain fatty-acid oxidation, allosterically inhibited by malonyl-CoA. Deficiency causes CPT1A deficiency. Muscle/brain use the CPT1B/CPT1C isoforms.

Carnitine acetyltransferases forming acetylcarnitine (fungi)Reactioncat_acetyl_variant

Annotons

CAT2 (peroxisomal) / YAT1 / YAT2: carnitine O-acetyltransferase
cat_acetyl_donor_activity
Participant: Family: Carnitine O-acyltransferase family (acetyltransferase members)
Family:
Carnitine O-acyltransferase family (acetyltransferase members)
Representative Members: CAT2 (Saccharomyces cerevisiae; peroxisomal isoform)UniProtKB:P32796 YAT1 (Saccharomyces cerevisiae; mitochondrial outer membrane)UniProtKB:P80235 YAT2 (Saccharomyces cerevisiae; cytosolic)UniProtKB:P40017

Function

carnitine O-acetyltransferase activityGO:0004092
Substrates: acetyl-CoA L-carnitine
Products: O-acetyl-L-carnitine coenzyme A

Convert acetyl-CoA made in the peroxisome (beta-oxidation) or cytosol (acetate/ethanol metabolism) to acetylcarnitine. The three paralogs act in different compartments and do not cross-complement (PMID:18427809), so no single location is asserted.

Part 3: acylcarnitine/carnitine antiport across the inner membrane
acylcarnitine (cytosolic side) / carnitine (matrix) antiportTransport Stepslc25a20_step

Annotons

SLC25A20/CACT, CRC1: carnitine/acylcarnitine translocase
slc25a20_activity
Participant: Family: Mitochondrial carnitine/acylcarnitine carrier family (SLC25A20, CRC1)
Family:
Mitochondrial carnitine/acylcarnitine carrier family (SLC25A20, CRC1)
Representative Members: SLC25A20 / CACT (human)UniProtKB:O43772 CRC1 (Saccharomyces cerevisiae)UniProtKB:Q12289

Function

O-acyl-L-carnitine transmembrane transporter activityGO:0015227
Substrates: acylcarnitine (long-chain in animals; acetylcarnitine in fungi), intermembrane space L-carnitine (matrix)
Products: acylcarnitine (matrix) L-carnitine (intermembrane space)

Locations

mitochondrial inner membraneGO:0005743

Inner-membrane antiporter importing acylcarnitine into the matrix in exchange for free carnitine. Substrate range differs by lineage (long-chain in animals, short-chain in yeast). SLC25A20 deficiency causes carnitine-acylcarnitine translocase deficiency.

Part 4: regeneration of matrix acyl-CoA (completes the shuttle)
acylcarnitine + CoA to acyl-CoA + L-carnitine (matrix)Reactioncpt2_step
Variant set: Matrix-side carnitine acyltransferase by cargo by acyl cargo (long-chain acyl vs acetyl) / lineage (One Or More)
CPT2 long-chain acyl transfer (animals)Reactioncpt2_long_chain_variant

Annotons

CPT2: carnitine palmitoyltransferase 2
cpt2_activity
Participant: Family: CPT2 carnitine O-palmitoyltransferase subfamily
Family:
CPT2 carnitine O-palmitoyltransferase subfamilyPANTHER:PTHR22589:SF51
Representative Members: CPT2 (human)UniProtKB:P23786

Function

carnitine O-palmitoyltransferase activityGO:0004095
Substrates: long-chain O-acylcarnitine (matrix) coenzyme A
Products: long-chain acyl-CoA L-carnitine

Locations

mitochondrial inner membraneGO:0005743

Matrix-facing inner-membrane transferase regenerating long-chain acyl-CoA for beta-oxidation. Deficiency causes CPT2 deficiency (myopathic form: exercise-induced rhabdomyolysis).

Mitochondrial carnitine acetyltransferase regenerating acetyl-CoA (fungi)Reactioncat2_mito_acetyl_variant

Annotons

CAT2 (mitochondrial isoform): carnitine O-acetyltransferase
cat2_mito_activity
Participant: Family: CAT2 mitochondrial/peroxisomal carnitine O-acetyltransferase subfamily
Family:
CAT2 mitochondrial/peroxisomal carnitine O-acetyltransferase subfamilyPANTHER:PTHR22589:SF103
Representative Members: CAT2 (Saccharomyces cerevisiae; mitochondrial isoform)UniProtKB:P32796

Function

carnitine O-acetyltransferase activityGO:0004092
Substrates: O-acetyl-L-carnitine (matrix) coenzyme A
Products: acetyl-CoA L-carnitine

Locations

mitochondrionGO:0005739

Regenerate matrix acetyl-CoA (for citrate synthase) and free carnitine for export by the translocase.