SHM1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003729 mRNA binding	IDA PMID:32344669 Discovering the RNA-Binding Proteome of Plant Leaves with an...	KEEP AS NON CORE	Summary: SHM1 was recovered in a proteome-wide leaf RNA interactome capture screen, which also recovered many metabolic enzymes that lack canonical RNA-binding domains. Reason: In vivo crosslinking is experimental evidence for RNA association, but no specific RNA target or function has been shown for this mitochondrial enzyme. The observation is kept as non-core. Supporting Evidence: PMID:32344669 a large proportion of leaf RBPs lack known RNA-binding domains, suggesting unconventional modes of RNA binding
GO:0004372 glycine hydroxymethyltransferase activity	IBA GO_REF:0000033	ACCEPT	Summary: Glycine hydroxymethyltransferase (SHMT) activity inherited from the ancestral SHMT node, which is seeded by characterized SHMTs from bacteria to mammals and by Arabidopsis SHMs. Reason: This is the defining catalytic activity of SHM1. SHMT activity is conserved across the family, and SHM1 retains the PLP-binding lysine region. At4g37930 appearing among the IBA sources reflects its own experimental annotation and is not circular. Supporting Evidence: PMID:22303256 The photorespiratory SHM enzyme (EC. 2.1.2.1) is encoded by a single gene (At4g37930) in Arabidopsis. PMID:16339799 is defective in mitochondrial SHMT activity and displays a lethal photorespiratory phenotype when grown at ambient CO2
GO:0004372 glycine hydroxymethyltransferase activity	IDA PMID:21976482 The presequence of Arabidopsis serine hydroxymethyltransfera...	ACCEPT	Summary: SHMT activity assigned from the Engel et al. SHM1/SHM2 study. UniProt cites this paper as experimental evidence for EC 2.1.2.1. Only the abstract is cached. Reason: UniProt records the catalytic activity with experimental evidence from this paper. The abstract describes SHM1 as the photorespiratory isozyme. We defer to the curator, who read the full text. Supporting Evidence: PMID:21976482 SHM1 has been identified as the photorespiratory isozyme file:ARATH/SHM1/SHM1-uniprot.txt EC=2.1.2.1 {ECO:0000269\|PubMed:21976482}
GO:0004372 glycine hydroxymethyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: SHMT activity inferred from the InterPro SHMT signature and the RHEA:15481 mapping. Reason: Consistent with the IBA and experimental rows. Supporting Evidence: file:ARATH/SHM1/SHM1-uniprot.txt SIMILARITY: Belongs to the SHMT family.
GO:0004372 glycine hydroxymethyltransferase activity	TAS PMID:9232907 Photosynthesis and fluorescence quenching, and the mRNA leve...	ACCEPT	Summary: Traceable author statement that the stm mutant is SHMT-deficient. Reason: The paper relies on the SHMT-deficient stm (shm1-1) mutant, which was later shown to be mutated in SHM1. This is consistent with the experimental activity evidence. Supporting Evidence: PMID:9232907 conditionally lethal serine hydroxymethyltransferase (SHMT)-deficient stm mutant
GO:0005515 protein binding	IPI PMID:19223513 Arabidopsis photorespiratory serine hydroxymethyltransferase...	REMOVE	Summary: SHM1 (SHMT1) interacts physically with mitochondrially targeted Fd-GOGAT (GLU1). The interaction is needed for photorespiratory SHMT activity. Reason: Bare protein binding is uninformative under the protein-binding policy. The interaction is real and functionally important, but it is a property of GLU1 regulating SHM1, and no more specific molecular function of SHM1 is shown. The interaction is recorded in the notes and the summary. Removing the term does not mean the interaction is false. Supporting Evidence: PMID:19223513 In the mitochondria, Fd-GOGAT interacts physically with SHMT1, and this interaction is necessary for photorespiratory SHMT activity.
GO:0005515 protein binding	IPI PMID:23232097 Ubiquitin-specific protease16 modulates salt tolerance in Ar...	REMOVE	Summary: SHM1 was identified as an interactor and substrate of the deubiquitinase UBP16 by yeast two-hybrid screening. Reason: Bare protein binding is uninformative. In this interaction SHM1 is the substrate whose ubiquitin is removed by UBP16, so no informative SHM1 molecular function follows from it. Removing the term does not mean the interaction is false. Supporting Evidence: PMID:23232097 We found that SHM1 is degraded in a 26S proteasome-dependent process, and UBP16 stabilizes SHM1 by removing the conjugated ubiquitin.
GO:0005634 nucleus	HDA PMID:14617066 Analysis of the Arabidopsis nuclear proteome and its respons...	MARK AS OVER ANNOTATED	Summary: Detected in a 2D-gel nuclear proteome of Arabidopsis. Reason: SHM1 is an abundant mitochondrial matrix enzyme with a mitochondrial transit peptide. No targeted study supports a nuclear pool, and gel-based organelle proteomes routinely include abundant contaminants. SHMT carries over into other fractions; for example it is a listed contaminant of complex I preparations. Supporting Evidence: PMID:20197505 a few contaminating proteins like prohibitin, the β-subunit of ATP synthase (complex V), Ser hydroxymethyltransferase, and lipoamide dehydrogenase
GO:0005737 cytoplasm	IEA GO_REF:0000044	TOO GENERAL	Summary: Cytoplasm, mapped from the UniProt subcellular-location line, which lists Mitochondrion and Cytoplasm. Reason: True but uninformative. The mitochondrion, which is part of the cytoplasm, is accepted for SHM1 from many experimental rows. A possible cytosolic pool is covered by the cytosol rows. Supporting Evidence: file:ARATH/SHM1/SHM1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion
GO:0005739 mitochondrion	HDA PMID:14671022 Experimental analysis of the Arabidopsis mitochondrial prote...	ACCEPT	Summary: Detected in the LC-MS/MS mitochondrial proteome. Reason: Consistent with the transit peptide, the mitochondrial SHMT activity deficit of shm1 mutants, and the targeted studies. Supporting Evidence: PMID:16339799 Mitochondrial serine hydroxymethyltransferase (SHMT), combined with glycine decarboxylase, catalyzes an essential sequence of the photorespiratory C2 cycle
GO:0005739 mitochondrion	HDA PMID:18385124 Heterogeneity of the mitochondrial proteome for photosynthet...	ACCEPT	Summary: Detected in shoot mitochondrial proteomes, which are enriched for photorespiratory machinery. Reason: Consistent with all other localization evidence. Supporting Evidence: PMID:18385124 showed the elevated level of the photorespiratory apparatus and its complex interplay with glycolate, cysteine, formate, and one-carbon metabolism
GO:0005739 mitochondrion	IBA GO_REF:0000033	ACCEPT	Summary: Mitochondrial activity location inherited from the mitochondrial SHMT clade node. Reason: SHM1 belongs to the mitochondrial SHMT subfamily (PTHR11680:SF61) and has an N-terminal transit peptide. Its own experimental mitochondrial annotations are among the descendant evidences for this node. Supporting Evidence: PMID:10806255 Both SHM1 and SHM2 protein products are predicted to be targeted into the mitochondrial matrix.
GO:0005739 mitochondrion	IDA PMID:19223513 Arabidopsis photorespiratory serine hydroxymethyltransferase...	ACCEPT	Summary: Mitochondrial location of SHMT1 shown in the GLU1/Fd-GOGAT study, where the interaction with GLU1 takes place in mitochondria. Reason: This is direct experimental evidence and agrees with all other data. Supporting Evidence: PMID:19223513 SHM1, which encodes the mitochondrial SHMT required for photorespiration
GO:0005739 mitochondrion	IDA PMID:23232097 Ubiquitin-specific protease16 modulates salt tolerance in Ar...	ACCEPT	Summary: Mitochondrial location of SHM1 assigned from the UBP16 study. Only the abstract is cached. Reason: This agrees with all other evidence, so we defer to the curator. Supporting Evidence: PMID:23232097 SERINE HYDROXYMETHYLTRANSFERASE1 (SHM1), which has previously been reported to be involved in photorespiration and salt tolerance in Arabidopsis
GO:0005739 mitochondrion	IEA GO_REF:0000044	ACCEPT	Summary: Mitochondrion from the UniProt subcellular-location mapping. Reason: Consistent with the experimental evidence. Supporting Evidence: file:ARATH/SHM1/SHM1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion
GO:0005759 mitochondrial matrix	ISS PMID:10806255 Integrated temporal regulation of the photorespiratory pathw...	ACCEPT	Summary: Mitochondrial matrix location based on the predicted N-terminal mitochondrial targeting presequence. Reason: Mitochondrial SHMT is a soluble matrix enzyme that works with the matrix glycine decarboxylase complex. The matrix location matches the C2 cycle module and is the most specific location supported. Supporting Evidence: PMID:10806255 Both SHM1 and SHM2 protein products are predicted to be targeted into the mitochondrial matrix.
GO:0005829 cytosol	HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co...	KEEP AS NON CORE	Summary: Cytosol assignment from leaf protein-complex profiling by size-exclusion chromatography of total leaf extracts. Reason: Size-exclusion profiling of total leaf extracts cannot distinguish a genuine cytosolic pool from matrix protein released when organelles break. A cytosolic pool is plausible, however, because SHM1 is ubiquitinated and turned over by the 26S proteasome, and cytosol is also reported by IDA. This row is treated like the IDA row: kept, but not where SHM1 performs its photorespiratory function. Supporting Evidence: PMID:23232097 We found that SHM1 is degraded in a 26S proteasome-dependent process
GO:0005829 cytosol	IDA PMID:23232097 Ubiquitin-specific protease16 modulates salt tolerance in Ar...	KEEP AS NON CORE	Summary: Cytosolic SHM1 reported in the UBP16 study. Only the abstract is cached. Reason: We cannot see the localization data, but a cytosolic pool is plausible because SHM1 is ubiquitinated and degraded by the 26S proteasome, and UniProt also lists Cytoplasm. The cytosol is not where SHM1 performs its photorespiratory function, so the row is kept as non-core. Supporting Evidence: PMID:23232097 We found that SHM1 is degraded in a 26S proteasome-dependent process
GO:0005886 plasma membrane	HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati...	MARK AS OVER ANNOTATED	Summary: Plasma membrane assignment from membrane-associated protein correlation profiling. Reason: SHM1 is a soluble mitochondrial matrix enzyme without transmembrane segments. A plasma membrane call from fractionation-based profiling most likely reflects carry-over. Supporting Evidence: PMID:10806255 Both SHM1 and SHM2 protein products are predicted to be targeted into the mitochondrial matrix.
GO:0006544 glycine metabolic process	IDA PMID:21976482 The presequence of Arabidopsis serine hydroxymethyltransfera...	ACCEPT	Summary: Glycine metabolic process, based on the SHMT activity and the glycine accumulation of shm mutants. Reason: SHMT reversibly interconverts glycine and serine. SHM1 consumes glycine in photorespiration and works with SHM2 in one-carbon metabolism of vascular cells. Because the reaction runs in different directions in different cell types, glycine metabolic process is as precise as the evidence warrants. Supporting Evidence: PMID:21976482 Serine hydroxymethyltransferases (SHMs) are important enzymes of cellular one-carbon metabolism and are essential for the photorespiratory glycine-into-serine conversion in leaf mesophyll mitochondria.
GO:0006545 glycine biosynthetic process	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Glycine biosynthetic process inherited from the SHMT family node, reflecting the serine-to-glycine direction that dominates in heterotrophic cells. Reason: The SHMT reaction is reversible. In photosynthetic mesophyll SHM1 runs in the glycine-consuming, serine-forming direction, so glycine synthesis is not its core role. SHM1 also acts with SHM2 in one-carbon metabolism of non-photorespiring vascular cells, where serine cleavage yields glycine and methylene-THF. The term is therefore plausible but peripheral. Supporting Evidence: PMID:21976482 It seems that SHM1 and SHM2 operate in a redundant manner in one-carbon metabolism of nonphotorespiring cells with a high demand of one-carbon units; for example, during lignification of vascular cells.
GO:0006545 glycine biosynthetic process	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: Glycine biosynthetic process inferred from the InterPro SHMT signature. Reason: Same reasoning as the IBA row. This is a reversible-reaction mapping that is peripheral for the photorespiratory isozyme. Supporting Evidence: PMID:21976482 It seems that SHM1 and SHM2 operate in a redundant manner in one-carbon metabolism of nonphotorespiring cells with a high demand of one-carbon units; for example, during lignification of vascular cells.
GO:0006563 L-serine metabolic process	IDA PMID:21976482 The presequence of Arabidopsis serine hydroxymethyltransfera...	ACCEPT	Summary: L-serine metabolic process, based on the SHMT activity. Reason: Serine formation from glycine is the photorespiratory output of SHM1. Given the reversible reaction, serine metabolic process is an appropriate level. Supporting Evidence: PMID:21976482 are essential for the photorespiratory glycine-into-serine conversion in leaf mesophyll mitochondria
GO:0007623 circadian rhythm	IEP PMID:10806255 Integrated temporal regulation of the photorespiratory pathw...	MARK AS OVER ANNOTATED	Summary: SHM1 mRNA oscillates with a circadian rhythm in phase with other photorespiratory genes. Reason: The evidence shows clock control of SHM1 transcript abundance, an expression pattern. SHM1 is a clock output, not a component of the circadian oscillator, so it does not take part in the circadian rhythm process itself. Supporting Evidence: PMID:10806255 show that both exhibit circadian oscillations in mRNA abundance that are in phase with those described for other photorespiratory genes
GO:0008266 poly(U) RNA binding	IDA PMID:17511964 Identification of proteins expressed at extremely low level ...	MARK AS OVER ANNOTATED	Summary: SHM1 was enriched on a poly(U)-affinity column from leaf extracts. Reason: Retention on poly(U) resin from a crude extract was used to enrich proteins with nucleotide-binding motifs. It does not show sequence-specific or physiological RNA binding by a mitochondrial metabolic enzyme. The broader in vivo mRNA crosslinking evidence is kept as non-core. Supporting Evidence: PMID:17511964 Here we use a polyU-affinity column to enrich proteins with nucleotide-binding motifs.
GO:0009409 response to cold	IEP PMID:16923014 The chloroplast lumen and stromal proteomes of Arabidopsis t...	MARK AS OVER ANNOTATED	Summary: SHM1 abundance changed in chloroplast stromal proteomes during cold acclimation. Reason: This is an abundance change measured in chloroplast fractions, where SHM1 is most likely a contaminant. It is an expression response, not evidence that SHM1 takes part in a cold-response mechanism. Supporting Evidence: PMID:16923014 we have taken a proteomic approach (difference gel electrophoresis) to identify proteins that changed in abundance in Arabidopsis chloroplasts during cold shock
GO:0009416 response to light stimulus	IEP PMID:10806255 Integrated temporal regulation of the photorespiratory pathw...	MARK AS OVER ANNOTATED	Summary: SHM1 mRNA accumulates in light-grown seedlings. Reason: The authors interpret the light induction as an indirect consequence of photosynthesis and photorespiration. This is an expression response, not a role of SHM1 in sensing or responding to light. Supporting Evidence: PMID:10806255 this response is probably an indirect consequence of the induction of photosynthesis and photorespiration by illumination
GO:0009534 chloroplast thylakoid	HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit...	MARK AS OVER ANNOTATED	Summary: Assigned to thylakoids in the AT_CHLORO chloroplast proteome database. Reason: A soluble mitochondrial matrix enzyme. Detection in chloroplast subfractions most likely reflects mitochondrial contamination; large chloroplast proteomes acknowledge hundreds of such contaminants. Supporting Evidence: PMID:18431481 from manual evaluation we estimate that 300–350 proteins likely represent false positive identifications and/or non-chloroplast contaminations
GO:0009570 chloroplast stroma	HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit...	MARK AS OVER ANNOTATED	Summary: Assigned to stroma in the AT_CHLORO chloroplast proteome database. Reason: As for the thylakoid row, this most likely reflects mitochondrial carry-over of this abundant leaf enzyme. Supporting Evidence: PMID:18431481 from manual evaluation we estimate that 300–350 proteins likely represent false positive identifications and/or non-chloroplast contaminations
GO:0009626 plant-type hypersensitive response	TAS PMID:15659103 Arabidopsis SHMT1, a serine hydroxymethyltransferase that fu...	KEEP AS NON CORE	Summary: The weak shmt1-1 allele causes aberrant cell-death control, lesions and greater susceptibility to pathogens. Reason: The phenotype is real, and the acts-upstream relationship is appropriate. It is an indirect consequence of impaired photorespiratory flux and ROS accumulation, not a defence-signalling function of SHM1, so it is non-core. Supporting Evidence: PMID:15659103 this enzymatic activity plays a critical role in controlling the cell damage provoked by abiotic stresses such as high light and salt and in restricting pathogen-induced cell death
GO:0009853 photorespiration	IMP PMID:16339799 The photorespiratory Arabidopsis shm1 mutant is deficient in...	ACCEPT	Summary: shm1-1 and shm1-2 lack mitochondrial SHMT activity and show a conditional lethal photorespiratory phenotype. Expressing SHM1 complements the mutant. Reason: This is the core biological role of SHM1. It catalyses the serine-forming step of the photorespiratory C2 cycle, as shown by mutant mapping, an allelic series and complementation. Supporting Evidence: PMID:16339799 Mitochondrial serine hydroxymethyltransferase (SHMT), combined with glycine decarboxylase, catalyzes an essential sequence of the photorespiratory C2 cycle, namely, the conversion of two molecules of glycine into one molecule each of CO2, NH4+, and serine. PMID:16339799 Expression of wild-type SHM1 under the control of either the cauliflower mosaic virus 35S or the SHM1 promoter in shm1-1 abrogated the photorespiratory phenotype of the shm mutant
GO:0009853 photorespiration	IMP PMID:17400706 Impairment of the photorespiratory pathway accelerates photo...	ACCEPT	Summary: The SHMT-deficient mutant is among the photorespiratory mutants that show accelerated PSII photoinhibition because D1 repair is suppressed. Reason: This confirms that SHMT loss impairs the photorespiratory pathway. It is consistent with the core photorespiration annotation. Supporting Evidence: PMID:17400706 mutants of Arabidopsis (Arabidopsis thaliana) with impairment of ferredoxin-dependent glutamate synthase, serine hydroxymethyltransferase, glutamate/malate transporter, and glycerate kinase had accelerated photoinhibition of PSII
GO:0010319 stromule	IDA PMID:16923014 The chloroplast lumen and stromal proteomes of Arabidopsis t...	MARK AS OVER ANNOTATED	Summary: Stromule location assigned from a chloroplast stroma/lumen DIGE proteomics study. Only the abstract is cached. Reason: The study analysed isolated chloroplast stroma and lumen and did not image stromules. SHM1 is a mitochondrial matrix enzyme, and its presence in stromal preparations is best explained by contamination, so a stromule location is not supported. Supporting Evidence: PMID:16923014 To understand how the stroma and the lumen proteomes adapt to low temperatures
GO:0022626 cytosolic ribosome	HDA PMID:15821981 High heterogeneity within the ribosomal proteins of the Arab...	MARK AS OVER ANNOTATED	Summary: Co-migrated with cytoplasmic 80S ribosomes in a ribosome proteomics study. Reason: The authors describe co-migrating non-ribosomal proteins only as possible associations. A tetrameric matrix enzyme co-sedimenting with ribosomes does not establish a ribosomal location. Supporting Evidence: PMID:15821981 we have identified a number of non-ribosomal proteins that co-migrate with the plant 80S ribosomes during gradient centrifugation
GO:0030170 pyridoxal phosphate binding	IBA GO_REF:0000033	ACCEPT	Summary: Pyridoxal phosphate binding, the cofactor of SHMT, inherited from the SHMT family node. Reason: PLP is the obligatory cofactor of SHMT catalysis, and the PLP-binding site is conserved in SHM1. Supporting Evidence: file:ARATH/SHM1/SHM1-uniprot.txt Name=pyridoxal 5'-phosphate
GO:0030170 pyridoxal phosphate binding	IEA GO_REF:0000002	ACCEPT	Summary: PLP binding inferred from the InterPro SHMT and SHMT PLP-binding-site signatures. Reason: Consistent with the IBA row. Supporting Evidence: file:ARATH/SHM1/SHM1-uniprot.txt Name=pyridoxal 5'-phosphate
GO:0035999 folate cycle	IEA GO_REF:0000120	ACCEPT	Summary: Tetrahydrofolate interconversion (the folate cycle), inferred from the SHMT signature and UniPathway. Reason: SHMT interconverts THF and 5,10-methylene-THF. In photorespiration SHM1 regenerates THF from the methylene-THF produced by GDC, so it directly catalyses a step of THF interconversion. Supporting Evidence: PMID:22303256 The latter is used by SHM as a substrate for the transfer of an activated C1 moiety to another molecule of glycine resulting in the formation of serine. file:ARATH/SHM1/SHM1-uniprot.txt PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
GO:0046653 tetrahydrofolate metabolic process	IBA GO_REF:0000033	ACCEPT	Summary: Tetrahydrofolate metabolic process inherited from the SHMT family node. Reason: Correct. SHMT is a central enzyme of folate-dependent one-carbon metabolism, and SHM1 and SHM2 act redundantly in one-carbon metabolism of vascular cells. The term is broader than the accepted tetrahydrofolate interconversion but still informative at the pathway level. Supporting Evidence: PMID:21976482 Serine hydroxymethyltransferases (SHMs) are important enzymes of cellular one-carbon metabolism
GO:0048046 apoplast	HDA PMID:18538804 Hydroponic isotope labelling of entire plants (HILEP) for qu...	MARK AS OVER ANNOTATED	Summary: Apoplast assignment from a whole-plant quantitative proteomics (HILEP) study. Reason: The study is a method paper on whole-plant extracts (abstract only) and gives no evidence for secretion of this mitochondrial matrix enzyme. Supporting Evidence: file:ARATH/SHM1/SHM1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion

Gene Description

Existing Annotations Review

Core Functions

Mitochondrial serine hydroxymethyltransferase that converts glycine and GDC-derived 5,10-methylene-THF into L-serine and THF in the photorespiratory C2 cycle of leaf mesophyll mitochondria.

Together with SHM2, mitochondrial one-carbon metabolism in non-photorespiring (vascular) cells with a high demand for one-carbon units.

References

Suggested Questions for Experts

Suggested Experiments

📚 Additional Documentation

Notes

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