CoP: Co-expressed Biological Processes

Biological process to genes

Query process ID GO:0009853

Process name A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.

Organism Arabidopsis thaliana

Click Gene ID to show a list of co-expressed genes.

ECC Gene ID Repr. ID Gene name Functional description O.I. H.G. Other DB
X At1g23310 838940 GGT1 (GLUTAMATE:GLYOXYLATE AMINOTRANSFERASE) Identified by cloning the gene that corresponded to a purified protein having glyoxylate aminotransferase activity. Localized to the peroxisome and thought to be involved in photorespiration/ metabolic salvage pathway. O.I. H.G.
X At1g80380 844378 phosphoribulokinase/uridine kinase-related encodes a glycerate kinase which catalyzes the last step of photorespiration C2 cycle. O.I. H.G.
X At2g26350 817175 PEX10 Zinc-binding peroxisomal integral membrane protein (PEX10). Inserted directly from the cytosol into peroxisomes and is involved in importing proteins into the peroxisome. Required for embryogenesis. O.I. H.G.
X At3g54110 824578 PUMP1 (PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 1) Member of Uncoupling protein PUMP2 family. Encodes a mitochondrial uncoupling protein AtUCP1 involved in maintain the redox poise of the mitochondrial electron transport chain to facilitate photosynthetic metabolism. Disruption of UCP1 results in a photosynthetic phenotype. Specifically there is a restriction in photorespiration with a decrease in the rate of oxidation of photorespiratory glycine in the mitochondrion. This change leads to an associated reduced photosynthetic carbon assimilation rate. O.I. H.G.
X At4g17360 827448 formyltetrahydrofolate deformylase/ hydroxymethyl-, formyl- and related transferase/ methyltransferase encodes one of the two putative formyltetrahydrofolate deformylase. Located in the mitochondrion. Involved in photorespiratory tetrahydrofolate cycle. O.I. H.G.
X At4g37930 829949 SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1) Encodes a protein with mitochondrial serine hydroxymethyltransferase activity, which functions in the photorespiratory pathway, catalyzes the conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. Involved in controlling cell damage caused by abiotic stress, such as high light and salt and the hypersensitive defense response of plants. O.I. H.G.
X At5g04140 830292 GLU1 (GLUTAMATE SYNTHASE 1) Encodes a gene whose sequence is similar to ferredoxin dependent glutamate synthase (Fd-GOGAT). Expression in leaves is induced by light and sucrose. Proposed to be involved in photorespiration and nitrogen assimilation. O.I. H.G.
X At5g47435 834791 formyltetrahydrofolate deformylase, putative encodes one of the two putative formyltetrahydrofolate deformylase. Located in the mitochondrion. Involved in photorespiratory tetrahydrofolate cycle. O.I. H.G.
S At1g04630 839465 MEE4 (maternal effect embryo arrest 4) F:molecular_function unknown;P:embryonic development ending in seed dormancy, photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;MFPO O.I. H.G.
S At1g14450 838007 unknown protein F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;PF O.I. H.G.
S At1g19580 838545 GAMMA CA1 (GAMMA CARBONIC ANHYDRASE 1) Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex. O.I. H.G.
S At1g47260 841129 GAMMA CA2 (GAMMA CARBONIC ANHYDRASE 2) Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex. O.I. H.G.
S At1g49140 841337 NADH-ubiquinone oxidoreductase-related F:unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPM O.I. H.G.
S At1g67350 843056 unknown protein F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;P O.I. H.G.
S At1g68010 843129 HPR Encodes hydroxypyruvate reductase. O.I. H.G.
S At2g02050 814736 NADH-ubiquinone oxidoreductase B18 subunit, putative F:NADH dehydrogenase activity, NADH dehydrogenase (ubiquinone) activity;P:mitochondrial electron transport, NADH to ubiquinone, photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;MFPO O.I. H.G.
S At2g27730 817319 unknown protein F:molecular_function unknown;P:photorespiration;C:mitochondrion, nucleolus, mitochondrial membrane, vacuole, respiratory chain complex I;P O.I. H.G.
S At2g31490 817707 unknown protein F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;P O.I. H.G.
S At2g33220 817884 - F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, plastid, respiratory chain complex I;MFPO O.I. H.G.
S At2g35370 818104 GDCH Encodes glycine decarboxylase complex H protein. Involved in photorespiration. O.I. H.G.
S At2g47690 819382 NADH-ubiquinone oxidoreductase-related F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPOM O.I. H.G.
S At3g18410 821370 NADH-ubiquinone oxidoreductase-related F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPM O.I. H.G.
S At3g48680 824029 GAMMA CAL2 (GAMMA CARBONIC ANHYDRASE-LIKE 2) Encodes a mitochondrial gamma carbonic anhydrase-like protein. Component of the NADH dehydrogenase complex. O.I. H.G.
S At4g00585 828026 unknown protein F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;PFMO O.I. H.G.
S At4g16450 827343 unknown protein F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I, membrane;FP O.I. H.G.
S At4g34700 829622 complex 1 family protein / LVR family protein F:catalytic activity;P:photorespiration;C:mitochondrial membrane, plasma membrane, respiratory chain complex I;MFPO O.I. H.G.
S At5g37510 833729 EMB1467 (embryo defective 1467) Encodes a subunit of the 400 kDa subcomplex of the mitochondrial NADH dehydrogenase (complex I). The protein has been isolated in the male gametophyte. O.I. H.G.
S At5g52840 835361 NADH-ubiquinone oxidoreductase-related F:oxidoreductase activity, acting on NADH or NADPH;P:photorespiration;C:mitochondrion, mitochondrial membrane, chloroplast, respiratory chain complex I, membrane;MFPO O.I. H.G.
S At5g63510 836470 GAMMA CAL1 (GAMMA CARBONIC ANHYDRASE LIKE 1) Encodes a mitochondrial gamma carbonic anhydrase-like protein. Component of the NADH dehydrogenase complex. O.I. H.G.
S At5g66510 836783 GAMMA CA3 (GAMMA CARBONIC ANHYDRASE 3) Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex. O.I. H.G.
S Atmg01120 - Encodes subunit of mitochondrial NAD(P)H dehydrogenase that is trans-spliced from three precursors, NAD1A, NAD1B, and NAD1C. O.I. H.G.
C At1g70580 843395 AOAT2 (ALANINE-2-OXOGLUTARATE AMINOTRANSFERASE 2) Similar to glutamate-glyoxylate transaminase enzyme encoded by AOAT1 O.I. H.G.
N At2g13360 815822 AGT (ALANINE:GLYOXYLATE AMINOTRANSFERASE) Encodes a peroxisomal photorespiratory enzyme that catalyzes transamination reactions with multiple substrates. It is involved in photorespiration. O.I. H.G.

ECC	Gene ID	Repr. ID	Gene name	Functional description	O.I.	H.G.
X	At1g23310	838940	GGT1 (GLUTAMATE:GLYOXYLATE AMINOTRANSFERASE)	Identified by cloning the gene that corresponded to a purified protein having glyoxylate aminotransferase activity. Localized to the peroxisome and thought to be involved in photorespiration/ metabolic salvage pathway.	O.I.	H.G.
X	At1g80380	844378	phosphoribulokinase/uridine kinase-related	encodes a glycerate kinase which catalyzes the last step of photorespiration C2 cycle.	O.I.	H.G.
X	At2g26350	817175	PEX10	Zinc-binding peroxisomal integral membrane protein (PEX10). Inserted directly from the cytosol into peroxisomes and is involved in importing proteins into the peroxisome. Required for embryogenesis.	O.I.	H.G.
X	At3g54110	824578	PUMP1 (PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 1)	Member of Uncoupling protein PUMP2 family. Encodes a mitochondrial uncoupling protein AtUCP1 involved in maintain the redox poise of the mitochondrial electron transport chain to facilitate photosynthetic metabolism. Disruption of UCP1 results in a photosynthetic phenotype. Specifically there is a restriction in photorespiration with a decrease in the rate of oxidation of photorespiratory glycine in the mitochondrion. This change leads to an associated reduced photosynthetic carbon assimilation rate.	O.I.	H.G.
X	At4g17360	827448	formyltetrahydrofolate deformylase/ hydroxymethyl-, formyl- and related transferase/ methyltransferase	encodes one of the two putative formyltetrahydrofolate deformylase. Located in the mitochondrion. Involved in photorespiratory tetrahydrofolate cycle.	O.I.	H.G.
X	At4g37930	829949	SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)	Encodes a protein with mitochondrial serine hydroxymethyltransferase activity, which functions in the photorespiratory pathway, catalyzes the conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. Involved in controlling cell damage caused by abiotic stress, such as high light and salt and the hypersensitive defense response of plants.	O.I.	H.G.
X	At5g04140	830292	GLU1 (GLUTAMATE SYNTHASE 1)	Encodes a gene whose sequence is similar to ferredoxin dependent glutamate synthase (Fd-GOGAT). Expression in leaves is induced by light and sucrose. Proposed to be involved in photorespiration and nitrogen assimilation.	O.I.	H.G.
X	At5g47435	834791	formyltetrahydrofolate deformylase, putative	encodes one of the two putative formyltetrahydrofolate deformylase. Located in the mitochondrion. Involved in photorespiratory tetrahydrofolate cycle.	O.I.	H.G.
S	At1g04630	839465	MEE4 (maternal effect embryo arrest 4)	F:molecular_function unknown;P:embryonic development ending in seed dormancy, photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;MFPO	O.I.	H.G.
S	At1g14450	838007	unknown protein	F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;PF	O.I.	H.G.
S	At1g19580	838545	GAMMA CA1 (GAMMA CARBONIC ANHYDRASE 1)	Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex.	O.I.	H.G.
S	At1g47260	841129	GAMMA CA2 (GAMMA CARBONIC ANHYDRASE 2)	Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex.	O.I.	H.G.
S	At1g49140	841337	NADH-ubiquinone oxidoreductase-related	F:unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPM	O.I.	H.G.
S	At1g67350	843056	unknown protein	F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;P	O.I.	H.G.
S	At1g68010	843129	HPR	Encodes hydroxypyruvate reductase.	O.I.	H.G.
S	At2g02050	814736	NADH-ubiquinone oxidoreductase B18 subunit, putative	F:NADH dehydrogenase activity, NADH dehydrogenase (ubiquinone) activity;P:mitochondrial electron transport, NADH to ubiquinone, photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;MFPO	O.I.	H.G.
S	At2g27730	817319	unknown protein	F:molecular_function unknown;P:photorespiration;C:mitochondrion, nucleolus, mitochondrial membrane, vacuole, respiratory chain complex I;P	O.I.	H.G.
S	At2g31490	817707	unknown protein	F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;P	O.I.	H.G.
S	At2g33220	817884	-	F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, plastid, respiratory chain complex I;MFPO	O.I.	H.G.
S	At2g35370	818104	GDCH	Encodes glycine decarboxylase complex H protein. Involved in photorespiration.	O.I.	H.G.
S	At2g47690	819382	NADH-ubiquinone oxidoreductase-related	F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPOM	O.I.	H.G.
S	At3g18410	821370	NADH-ubiquinone oxidoreductase-related	F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPM	O.I.	H.G.
S	At3g48680	824029	GAMMA CAL2 (GAMMA CARBONIC ANHYDRASE-LIKE 2)	Encodes a mitochondrial gamma carbonic anhydrase-like protein. Component of the NADH dehydrogenase complex.	O.I.	H.G.
S	At4g00585	828026	unknown protein	F:molecular_function unknown;P:photorespiration;C:mitochondrial membrane, respiratory chain complex I;PFMO	O.I.	H.G.
S	At4g16450	827343	unknown protein	F:molecular_function unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I, membrane;FP	O.I.	H.G.
S	At4g34700	829622	complex 1 family protein / LVR family protein	F:catalytic activity;P:photorespiration;C:mitochondrial membrane, plasma membrane, respiratory chain complex I;MFPO	O.I.	H.G.
S	At5g37510	833729	EMB1467 (embryo defective 1467)	Encodes a subunit of the 400 kDa subcomplex of the mitochondrial NADH dehydrogenase (complex I). The protein has been isolated in the male gametophyte.	O.I.	H.G.
S	At5g52840	835361	NADH-ubiquinone oxidoreductase-related	F:oxidoreductase activity, acting on NADH or NADPH;P:photorespiration;C:mitochondrion, mitochondrial membrane, chloroplast, respiratory chain complex I, membrane;MFPO	O.I.	H.G.
S	At5g63510	836470	GAMMA CAL1 (GAMMA CARBONIC ANHYDRASE LIKE 1)	Encodes a mitochondrial gamma carbonic anhydrase-like protein. Component of the NADH dehydrogenase complex.	O.I.	H.G.
S	At5g66510	836783	GAMMA CA3 (GAMMA CARBONIC ANHYDRASE 3)	Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex.	O.I.	H.G.
S	Atmg01120		-	Encodes subunit of mitochondrial NAD(P)H dehydrogenase that is trans-spliced from three precursors, NAD1A, NAD1B, and NAD1C.	O.I.	H.G.
C	At1g70580	843395	AOAT2 (ALANINE-2-OXOGLUTARATE AMINOTRANSFERASE 2)	Similar to glutamate-glyoxylate transaminase enzyme encoded by AOAT1	O.I.	H.G.
N	At2g13360	815822	AGT (ALANINE:GLYOXYLATE AMINOTRANSFERASE)	Encodes a peroxisomal photorespiratory enzyme that catalyzes transamination reactions with multiple substrates. It is involved in photorespiration.	O.I.	H.G.

The upper GO terms

Process ID Gene number Process name
GO:0043094 0 Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.

Process ID	Gene number	Process name
GO:0043094	0	Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.

The lower GO terms

Process ID Gene number Process name
GO:0009854 0 The reactions of the C2 pathway bring about the metabolic conversion of two molecules of 2-phosphoglycolate to one molecule of 3-phosphoglycerate, which can be used by the C3 cycle, and one molecule of carbon dioxide (CO2).

Process ID	Gene number	Process name
GO:0009854	0	The reactions of the C2 pathway bring about the metabolic conversion of two molecules of 2-phosphoglycolate to one molecule of 3-phosphoglycerate, which can be used by the C3 cycle, and one molecule of carbon dioxide (CO2).

Comparison with co-expressed genes

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Query process ID	GO:0009853
Process name	A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.
Organism	Arabidopsis thaliana

Biological process to genes

The upper GO terms

Process ID Gene number Process name GO:00430940Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.

The lower GO terms

Process ID Gene number Process name GO:00098540The reactions of the C2 pathway bring about the metabolic conversion of two molecules of 2-phosphoglycolate to one molecule of 3-phosphoglycerate, which can be used by the C3 cycle, and one molecule of carbon dioxide (CO2).

Comparison with co-expressed genes

Process ID Gene number Process name
GO:0043094 0 Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.

Process ID Gene number Process name
GO:0009854 0 The reactions of the C2 pathway bring about the metabolic conversion of two molecules of 2-phosphoglycolate to one molecule of 3-phosphoglycerate, which can be used by the C3 cycle, and one molecule of carbon dioxide (CO2).