ALDH12A1

Summary: ALDH12A1 oxidizes glutamate semialdehyde/P5C to glutamate using NAD+.

Reason: Yeast put2 complementation and native isotope-proline degradation establish the P5CDH reaction; curated NAD+-dependent chemistry supports the existing cofactor-specific annotation. The 2001 paper cites comparative plant NAD preference, not purified Arabidopsis NAD-versus-NADP kinetics, so no absolute exclusion of NADP turnover is inferred.

Summary: ALDH12A1 oxidizes glutamate semialdehyde/P5C to glutamate using NAD+.

Reason: Yeast put2 complementation and native isotope-proline degradation establish the P5CDH reaction; curated NAD+-dependent chemistry supports the existing cofactor-specific annotation. The 2001 paper cites comparative plant NAD preference, not purified Arabidopsis NAD-versus-NADP kinetics, so no absolute exclusion of NADP turnover is inferred.

Summary: ALDH12A1 oxidizes glutamate semialdehyde/P5C to glutamate using NAD+.

Reason: Yeast put2 complementation and native isotope-proline degradation establish the P5CDH reaction; curated NAD+-dependent chemistry supports the existing cofactor-specific annotation. The 2001 paper cites comparative plant NAD preference, not purified Arabidopsis NAD-versus-NADP kinetics, so no absolute exclusion of NADP turnover is inferred.

Summary: Refine the broad oxidoreductase annotation to the supported P5CDH reaction.

Reason: The enzyme belongs to the aldehyde dehydrogenase family, but native function and complementation identify the GSA/P5C oxidation activity more precisely; GO:0003842 is already supported in this review.

Proposed replacements: L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity

Summary: Mitochondrial residence is a supported core localization.

Reason: The N-terminal GFP targeting experiment establishes mitochondrial localization in tobacco and Arabidopsis protoplasts (PMID:11532180), independently supporting the organelle claim. Retain mitochondrial residence alongside the existing matrix assignment. Neither the targeting assay nor each proteomic observation must resolve the subcompartment to support this retained annotation.

Summary: Mitochondrial residence is a supported core localization.

Reason: The N-terminal GFP targeting experiment establishes mitochondrial localization in tobacco and Arabidopsis protoplasts (PMID:11532180), independently supporting the organelle claim. Retain mitochondrial residence alongside the existing matrix assignment. Neither the targeting assay nor each proteomic observation must resolve the subcompartment to support this retained annotation.

Summary: Mitochondrial residence is a supported core localization.

Reason: The N-terminal GFP targeting experiment establishes mitochondrial localization in tobacco and Arabidopsis protoplasts (PMID:11532180), independently supporting the organelle claim. Retain mitochondrial residence alongside the existing matrix assignment. Neither the targeting assay nor each proteomic observation must resolve the subcompartment to support this retained annotation. The inherited organelle claim agrees with independent target evidence; no ancestral-node placement defect is established or inferred from its breadth.

Summary: Mitochondrial residence is a supported core localization.

Reason: The N-terminal GFP targeting experiment establishes mitochondrial localization in tobacco and Arabidopsis protoplasts (PMID:11532180), independently supporting the organelle claim. Retain mitochondrial residence alongside the existing matrix assignment. Neither the targeting assay nor each proteomic observation must resolve the subcompartment to support this retained annotation.

Summary: Mitochondrial residence is a supported core localization.

Reason: The N-terminal GFP targeting experiment establishes mitochondrial localization in tobacco and Arabidopsis protoplasts (PMID:11532180), independently supporting the organelle claim. Retain mitochondrial residence alongside the existing matrix assignment. Neither the targeting assay nor each proteomic observation must resolve the subcompartment to support this retained annotation. Independent target localization supports the transferred organelle claim without treating the computational row as a new direct experiment.

Summary: ALDH12A1 functions in the mitochondrial matrix catabolic pathway.

Reason: The curated matrix assignment is consistent with the mitochondrial targeting experiment and soluble plant P5CDH enzymology. The targeting fragment alone does not constitute a matrix-specific microscopy assay.

Summary: A stable extra-mitochondrial enzyme pool remains unresolved.

Reason: PMID:25293756 analyzes a crude soluble fraction, which can contain released organellar enzymes. In the independently inspected PMID:28887381 S1 supplement this target is assigned mitochondrion, not plastid; detection in the mixed preparation does not establish a plastid or cytosolic resident pool. Mitochondrial import does not by itself exclude dual localization, so these experimental annotations are not rejected.

Summary: Refine proline metabolism to proline catabolism.

Reason: Native isotope feeding establishes degradation to glutamate/glutamine and its loss in p5cdh; this is the supported direction already represented by GO:0006562.

Proposed replacements: L-proline catabolic process

Summary: P5CDH catalyzes the second step of proline degradation.

Reason: Native isotope-proline experiments and loss-of-function analysis show that this enzyme performs the oxidative conversion needed for degradation. The lack of a gross vegetative phenotype under ordinary growth does not negate the catalytic function.

Summary: P5CDH catalyzes the second step of proline degradation.

Reason: Native isotope-proline experiments and loss-of-function analysis show that this enzyme performs the oxidative conversion needed for degradation. The lack of a gross vegetative phenotype under ordinary growth does not negate the catalytic function.

Summary: The metal-affinity screen suggests association, but target-specific direct binding remains unresolved.

Reason: Full PMID:20018591 uses metal-loaded IMAC on mitochondrial extracts and identifies multiple proteins from enriched gel bands. This does not make metal binding false or require a physiological cofactor role; however, the exact target rows in supplemental S3/S4 could not be recovered, and direct binding versus co-purification is unresolved. Preserve the experimental annotation pending target-specific evidence rather than replacing it with the enzyme cofactor.

Summary: A stable extra-mitochondrial enzyme pool remains unresolved.

Reason: PMID:25293756 analyzes a crude soluble fraction, which can contain released organellar enzymes. In the independently inspected PMID:28887381 S1 supplement this target is assigned mitochondrion, not plastid; detection in the mixed preparation does not establish a plastid or cytosolic resident pool. Mitochondrial import does not by itself exclude dual localization, so these experimental annotations are not rejected.

Summary: P5CDH participates in a context-dependent salt-response metabolic circuit.

Reason: Full PMID:16377568 demonstrates salt-induced antisense regulation of P5CDH, altered proline pools and modest salt-tolerance changes in the mutant. The phenotype and regulatory sign vary with conditions; this is not an assertion that more P5CDH always improves salt tolerance.

Summary: Refine the broad oxidoreductase annotation to the supported P5CDH reaction.

Reason: The enzyme belongs to the aldehyde dehydrogenase family, but native function and complementation identify the GSA/P5C oxidation activity more precisely; GO:0003842 is already supported in this review.

Proposed replacements: L-glutamate gamma-semialdehyde dehydrogenase (NAD+) activity

Summary: P5CDH supports resource allocation and reserve accumulation during seed development.

Reason: PMID:36528796 directly compares allelic p5cdh mutants and measures carbon/nitrogen partitioning and 15N remobilization, with abnormal carbon-depleted seeds. This establishes a developmental consequence of enzyme-mediated resource remobilization rather than a dedicated patterning activity.

Summary: The metal-affinity screen suggests association, but target-specific direct binding remains unresolved.

Reason: Full PMID:20018591 uses metal-loaded IMAC on mitochondrial extracts and identifies multiple proteins from enriched gel bands. This does not make metal binding false or require a physiological cofactor role; however, the exact target rows in supplemental S3/S4 could not be recovered, and direct binding versus co-purification is unresolved. Preserve the experimental annotation pending target-specific evidence rather than replacing it with the enzyme cofactor.

Summary: P5CDH limits ROS production through control of proline/P5C metabolism.

Reason: Full PMID:16377568 and PMID:19635803 connect P5CDH loss to increased ROS and P5C-Pro cycling. P5CDH oxidizes GSA/P5C rather than directly consuming ROS; negative regulation of ROS metabolism expresses this supported causal role more precisely than direct ROS metabolism.

Proposed replacements: negative regulation of reactive oxygen species metabolic process