Link to pathway encoded in the SEED database
| Legend: | A yellow background indicates genes that are enigmatic in some way in plants | A light pink background indicates genes that are unknown in plants | A dark pink background indicates genes that are unknown in all organisms | A pale blue background indicates evidence that genes are not present in plants | A dark gray background indicates probable pseudogenes |
| Abbrev | AT gene ID | Gene name | Maize ortholog | Functional role | Curated localization | Localization data in AT | Localization data in maize | Experimental data | Problems, open questions, predictions |
|---|---|---|---|---|---|---|---|---|---|
| Pyrimidine moiety | |||||||||
| HMPPS | At2g29630 | ThiC | GRMZM2G027663 | Hydroxymethylpyrimidine phosphate synthase ThiC | # plastidial (experimental evidence in Arabidopsis and in maize) | Plastid - E [PMID:18048325] [PMID:18332905] | Plastid -E [PMID:20089766], PPDB in-house data. | At2g29630 complements E. coli thiC [PMID:18332905]. Evidence for involvement of an iron-sulfur cluster [PMID:18048325]. Regulated by a riboswitch in the 3'-untranslated region [PMID:18048325]. | |
| HMP(P)K/TMP-PPse | At1g22940 | ThiD/ThiE, TH1 | GRMZM2G401934 | Hydroxymethylpyrimidine phosphate kinase ThiD (EC 2.7.4.7) / Hydroxymethylpyrimidine kinase (EC 2.7.1.49) / Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3) | # plastidial (experimental evidence in Arabidopsis, bioinformatics evidence in maize) | Plastid - E [PMID:17174261] | Plastid - P [PMID:17696876] | Complementation in E. coli and Salmonella for Arabidopsis At1g22940 [PMID:17174261] and Brassica [PMID:9700068] cDNAs. Biochemical analysis of recombinant protein has been done only for maize; all 3 activities were shown [PMID:17696876]. | |
| Thiazole moiety | |||||||||
| Thi4 | At5g54770* | Thi4, Thi1, TZ | Thiazole biosynthetic enzyme Thi4 / Mitochondrial DNA damage tolerance | # plastidial (experimental evidence in Arabidopsis and maize) | Plastid - E [PMID:12482914] [PMID:11575719]. Mitochondrial localization also reported but evidence weak. | n/a | Both maize genes are expressed [PMID:8541506]. Maize GRMZM2G018375 [PMID:8541506] and Arabidopsis At5g54770 [PMID:8790291] cDNAs complemented the yeast THI4 mutant. Data implicating Arabidopsis At5g54770 in DNA damage tolerance: [PMID:8790291] [PMID:9367751]. | Yeast Thi4 serves as the sulfur donor in a single turnover reaction and is apparently not repaired [PMID:22031445]. It has been suggested that inactivated Thi4 could have physiological functions. HET-P was widely believed to be the product of Thi4, but recently the adenylated compound ADT was deduced to be the product [PMID:22031445] [PMID:19348578]. This implies existence of a hydrolase to convert ADT to HET-P [PMID:19348578]. This hypothesis has not been tested. | |
| Thi4 | GRMZM2G018375* | Thiazole biosynthetic enzyme Thi4 / Mitochondrial DNA damage tolerance | # plastidial (experimental evidence in Arabidopsis and maize) | Plastid - E. Protein detected in the plastid membrane fraction by immunobloting [PMID:8541506]; the mitochondrial fraction was not tested. Further evidence: [PMID:20089766] and PPDB in-house data. | Both maize genes are expressed [PMID:8541506]. Maize GRMZM2G018375 [PMID:8541506] and Arabidopsis At5g54770 [PMID:8790291] cDNAs complemented the yeast THI4 mutant. Data implicating Arabidopsis At5g54770 in DNA damage tolerance: [PMID:8790291] [PMID:9367751]. | Yeast Thi4 serves as the sulfur donor in a single turnover reaction and is apparently not repaired [PMID:22031445]. It has been suggested that inactivated Thi4 could have physiological functions. HET-P was widely believed to be the product of Thi4, but recently the adenylated compound ADT was deduced to be the product [PMID:22031445] [PMID:19348578]. This implies existence of a hydrolase to convert ADT to HET-P [PMID:19348578]. This hypothesis has not been tested. | |||
| Thi4 | GRMZM2G074097* | Thiazole biosynthetic enzyme Thi4 / Mitochondrial DNA damage tolerance | # plastidial (experimental evidence in Arabidopsis and maize) | Plastid - E. Protein detected in the plastid membrane fraction by immunobloting [PMID:8541506]; the mitochondrial fraction was not tested. Further evidence: [PMID:20089766] and PPDB in-house data. | Both maize genes are expressed [PMID:8541506]. Maize GRMZM2G018375 [PMID:8541506] and Arabidopsis At5g54770 [PMID:8790291] cDNAs complemented the yeast THI4 mutant. Data implicating Arabidopsis At5g54770 in DNA damage tolerance: [PMID:8790291] [PMID:9367751]. | Yeast Thi4 serves as the sulfur donor in a single turnover reaction and is apparently not repaired [PMID:22031445]. It has been suggested that inactivated Thi4 could have physiological functions. HET-P was widely believed to be the product of Thi4, but recently the adenylated compound ADT was deduced to be the product [PMID:22031445] [PMID:19348578]. This implies existence of a hydrolase to convert ADT to HET-P [PMID:19348578]. This hypothesis has not been tested. | |||
| Hydrolase | Globally missing gene | Hydrolase for conversion of ADT to HET-P | # plastidial (bioinformatic evidence in Arabidopsis) | Plastid - P (preceding and succeeding steps are plastidial) | The existence of this enzyme was suggested in [PMID:21904031]. No experimental biochemical or genetic data yet support this. | ||||
| Thiamin <-> ThMP <-> ThDP interconversions | |||||||||
| TPPK | At1g02880* | TPK1 | Thiamin pyrophosphokinase (EC 2.7.6.2) | # cytosolic (experimental evidence in Arabidopsis) | Cytosolic - E [PMID:17611796] | TPK1 and TPK2 are redundant: single gene knockouts of either gene are viable, but the double mutant has a seedling lethal phenotype [PMID:17611796]. Hence, TPK activity is the sole mechanism by which exogenous and de novo synthesized thiamin in plants is converted to the active cofactor ThDP [PMID:17611796]. Maize and soybean enzymes prefer GTP as a phosphate donor [Howle and Fites, 1991. Physiol. Plant. 81, 24-30]. | |||
| TPPK | At2g44750* | TPK2 | Thiamin pyrophosphokinase (EC 2.7.6.2) | # cytosolic (experimental evidence in Arabidopsis) | Cytosolic - E [PMID:17611796] | TPK1 and TPK2 are redundant: single gene knockouts of either gene are viable, but the double mutant has a seedling lethal phenotype [PMID:17611796]. Hence, TPK activity is the sole mechanism by which exogenous and de novo synthesized thiamin in plants is converted to the active cofactor ThDP [PMID:17611796]. Maize and soybean enzymes prefer GTP as a phosphate donor [Howle and Fites, 1991. Physiol. Plant. 81, 24-30]. | |||
| TPPK | GRMZM2G055458* | Thiamin pyrophosphokinase (EC 2.7.6.2) | # cytosolic (experimental evidence in Arabidopsis) | TPK1 and TPK2 are redundant: single gene knockouts of either gene are viable, but the double mutant has a seedling lethal phenotype [PMID:17611796]. Hence, TPK activity is the sole mechanism by which exogenous and de novo synthesized thiamin in plants is converted to the active cofactor ThDP [PMID:17611796]. Maize and soybean enzymes prefer GTP as a phosphate donor [Howle and Fites, 1991. Physiol. Plant. 81, 24-30]. | |||||
| TPPK | GRMZM5G864815* | Thiamin pyrophosphokinase (EC 2.7.6.2) | # cytosolic (experimental evidence in Arabidopsis) | TPK1 and TPK2 are redundant: single gene knockouts of either gene are viable, but the double mutant has a seedling lethal phenotype [PMID:17611796]. Hence, TPK activity is the sole mechanism by which exogenous and de novo synthesized thiamin in plants is converted to the active cofactor ThDP [PMID:17611796]. Maize and soybean enzymes prefer GTP as a phosphate donor [Howle and Fites, 1991. Physiol. Plant. 81, 24-30]. | |||||
| ThMPse | Globally missing gene | Thiamine-monophosphate phosphatase (EC 3.1.3.-) | # cytosolic and/or plastidial | Cytosolic or plastidial - P (related to whether plastids export thiamin or ThMP) | As ThMP is produced in plastids and ThDP is synthesized via thiamin in the cytosol, ThMPase activity presumably resides in plastids, the cytosol, or both. | ||||
| TPK | Probably non-existent | Thiamine-monophosphate kinase (EC 2.7.4.16) | # plastidial or cytosolic | Arabidopsis TPK1 TPK2 double knockouts have a seedling lethal phenotype, accumulate thiamin, are 97% depleted in ThDP, and are not rescued by thiamin or ThMP [PMID:17611796]. This implies that TPKs are the main if not the sole route for ThDP formation. Were thiamin and ThMP kinases involved in ThDP formation, supplied thiamin and ThMP should have rescued the lethal phenotype. | Available data [PMID:17611796] do not totally exclude the possibility that plastids have ThMP kinase activity because such an activity might fail to sustain TPK1 TPK2 double knockout plants when ThMP is supplied because of poor import of ThMP. Also, TPK1 TPK2 double knockout plants are not totally devoid of ThDP [PMID:17611796], which is consistent with the possibility of a minor TPK-independent route to ThDP. Plants have no homolog of bacterial ThMP kinase (ThiL). | ||||
| ThDP <-> ThTP interconversion | |||||||||
| ThTPS | Globally missing gene | Thiamine-triphosphate (ThTP) synthase (EC 2.7.4.15) | n/a | ThTP has been detected in Arabidopsis [PMID:12943234] and other plants [PMID:20655074], but neither biosynthetic nor ThTP-hydrolyzing enzymes have been studied in plants since a single early publication (Kikuchi and Ikawa, 1984. Bot. Mag. (Tokyo) 97,193-205]. | No sequences are associated with this function in any organism. Bettendorff et al. [PMID:19490098] [PMID:19906644] challenge earlier reports [PMID:6311826] [PMID:3034239] on enzymes with alleged ThTPS activity (in KEGG: EC 2.7.4.15). They argue that in rat brain at least this reaction is coupled to the respiratory chain, similar to that of ATP synthesis, and cannot be energized by ATP hydrolysis [PMID:19906644]. They suggest that ThTP synthesis by cytosolic adenylate kinase 1 (AK1; EC 2.7.4.3) reported eariler [PMID:2551297], as well as the cytosolic pool of ThTP, lack physiological significance [PMID:19906644]. | ||||
| ThTPse | Missing gene | Thiamine-triphosphatase (EC 3.6.1.28) | n/a | No data in plants. Membrane-bound ThTPases are present in many animal tissues [PMID:2547899] [PMID:4344228], but have not yet been purified. A soluble cytosolic ThTPase from bovine brain was characterized, it has near perfect specificity for ThTP [PMID:11827967]. Activities of two ThTPases, one membrane-bound and one soluble, similar to their rat tissue counterparts, have been detected in E. coli [PMID:3039089]. The only characterized bovine ThTPase [PMID:11827967] has no clear homologs outside mammals, however, the members of the ancient CYTH superfamily it belongs to are found in all kingdoms, including plants [PMID:12456267]. | No gene candidates in plants for a specific ThTPase. ThTP could be hydrolyzed by unspecific phosphohydrolases in plants and other organisms [PMID:12943234]. | ||||
| Catabolism and salvage of thiamin degradation products | |||||||||
| HET-K | At3g24030 | ThiM | GRMZM2G094558 | Hydroxyethylthiazole kinase (EC 2.7.1.50) | # cytosolic (bioinformatic evidence in Arabidopsis) | Cytosol - P (no predicted targeting signals) | The Arabidopsis and maize genes allow rescue of E. coli thiG thiM and thiH thiM double deletants by HET [R. Zallot, V. de Crecy-Lagard, A.D. Hanson, unpublished]. | The plant proteins lack a predicted plastid targeting sequence, yet their product, HET-P, is apparently utilized only in plastids. | |
| TenA1 | At5g32470 | TenA1 | GRMZM2G078283 | Thiaminase II (EC 3.5.99.2) involved in salvage of thiamin pyrimidine moiety / HAD hydrolase domain | unclear | Cytosol - E [PMID:21166475]. Mitochondrion - P (predicted mitochondrial targeting peptide in Arabidopsis and other plant sequences). | Fusion with a HAD hydrolase domain is specific to plants. There are no experimental data for the plant enzyme. The corresponding yeast enzyme (THII20) is involved in salvage of pyrimidine rather than in thiamin degradation [PMID:17618314] [PMID:21904031]. The Bacillus subtilis homolog (TenA) hydrolyses 4-amino-5-aminomethyl-2-methylpyrimidine, yielding HMP [PMID:18054064]. | Implicated in thiamin salvage based on gene clustering patterns of bacterial homologs. The TenA family consists of at least two branches with different substrate specificities, likely for various products of thiamin degradation [PMID:18054064] [PMID:19780837]. It is not clear from homology which subgroup the plant enzymes belong to. | |
| TenA1 | GRMZM2G148896 | unclear | |||||||
| TenA2 | At3g16990 | TenA2 | GRMZM2G080501 | TenA2, thiaminase II (EC 3.5.99.2) homolog involved in salvage of thiamin pyrimidine moiety | # cytosolic (bioinformatics evidence in Arabidopsis) | Cytosol - P (no predicted targeting signals) | Cytosol - P (TargetP); no exp. data available in PPDB. | Crystal structure is available: 1Q4M in PDB [PMID:15326608]. Ensemble-refined PDB entry 2Q4X [PMID:17850744] shows HMP as a ligand. At3g16990 belongs to a distinct subgroup of the TenA superfamily, distinct from those reported in [PMID:18054064] [PMID:19780837]. | Implicated in thiamin salvage based on bound HMP in the crystal structure and on gene clustering patterns of bacterial homologs. |
| NUDIX | At5g19460 | NUDT20 | GRMZM2G031461 | Nudix hydrolase, associated with thiamin pyrophosphokinase | # plastidial (experimental evidence in Arabidopsis) | Plastid - E [PMID:18815383] [PMID:18431481] | Substrate(s) of the NUDT20 and 24 are unknown. No activity was detected with dNTP, NAD(P)H, FAD, CoA, several UDP- or ADP-containing compounds [PMID:18815383]. | Arguments for an association with thiamin metabolism: NUDT20 and 24 are strong homologs of a Nudix domain fused to thiamin pyrophosphokinase Tnr3 in Schizosaccharomyces pombe. Also, a few bacterial homologs (in Neisseria and other Betaproteobacteria) colocalize with thiamin biosynthesis genes. NUDT20 and 24 are unlikely candidates for a missing ThMP phosphatase or for any other role in thiamin biosynthesis since strong homologs occur in organisms incapable of thiamin biosynthesis. They are also unlikely candidates for a proposed hydrolase converting the AMP adduct of thiazole phosphate (generated by THI4) to HET-P, since homologs occur in bacteria lacking a THI4-type pathway. A possible function is hydrolysis of degradation products such as phosphorylated oxothiamin or oxythiamin. | |
| NUDIX | At5g19470 | NUDT24 | Nudix hydrolase, associated with thiamin pyrophosphokinase | # plastidial (experimental evidence in Arabidopsis) | Plastid - E [PMID:18815383] | Substrate(s) of the NUDT20 and 24 are unknown. No activity was detected with dNTP, NAD(P)H, FAD, CoA, several UDP- or ADP-containing compounds [PMID:18815383]. | Arguments for an association with thiamin metabolism: NUDT20 and 24 are strong homologs of a Nudix domain fused to thiamin pyrophosphokinase Tnr3 in Schizosaccharomyces pombe. Also, a few bacterial homologs (in Neisseria and other Betaproteobacteria) colocalize with thiamin biosynthesis genes. NUDT20 and 24 are unlikely candidates for a missing ThMP phosphatase or for any other role in thiamin biosynthesis since strong homologs occur in organisms incapable of thiamin biosynthesis. They are also unlikely candidates for a proposed hydrolase converting the AMP adduct of thiazole phosphate (generated by THI4) to HET-P, since homologs occur in bacteria lacking a THI4-type pathway. A possible function is hydrolysis of degradation products such as phosphorylated oxothiamin or oxythiamin. | ||
| COG0212 | At1g76730 | GRMZM2G001904 | 5-Formyltetrahydrofolate cycloligase paralog implicated in thiamin metabolism | # plastidial (experimental evidence in Arabidopsis) | Plastid - E [PMID:21538139] [PMID:18431481] | The At1g76730 protein lacks 5-formyltetrahydrofolate cycloligase (5-FCL) activity and is required for embryo viability [PMID:21538139]. Comparative genomic and experimental evidence in prokaryotes point to a role in thiamin metabolism, probably in salvage or detoxification [PMID:21538139]. | Specific biological role is unclear: biochemical and genetic tests of several known and hypothetical thiamin-related activities (involving thiamin, its breakdown products, and their phosphates) were negative [PMID:21538139]. | ||
| Thiamin, ThDP, ThMP transport | |||||||||
| B1 transp | Missing gene | Plasma membrane thiamin transporter | # plasma membrane | Thiamin uptake by plants is well documented e.g. [PMID:17841380] [PMID:16653447] [PMID:15980201]. Supplementation with thiamin restores growth of Arabidopsis AtTHIC [PMID:18332905] and TH1 [PMID:5364924] mutants, implying the existence of a thiamin uptake system. Thiamin export is implied by the observation that roots depend on transport of thiamin from green tissues [PMID:20655074]. | No strong candidate genes suggested in plants. Human plasma membrane thiamin transporters SLC19A2 (THTR-1) and SLC19A3 (THTR-2) [PMID:10391221] [PMID:11731220] do not have clear homologs in Arabidopsis. Unrelated Saccharomyces cerevisiae [PMID:9235906] and Schizosaccharomyces pombe [PMID:18201975] thiamin transporters (THI10 and THI9) give weak hits on Arabidopsis proteins At5g03555 and At2g01170, respectively. However, these plant genes are unlikely candidates: they are not bidirectional best hits, and when used as queries against fungal genomes, appear to correspond to allantoin (YIR028W), uridine (YBL042C), or uracil (YBR021W) permeases (for At5g03555) or amino acid permeases (for At2g01170). | ||||
| ThMP or B1 transp | Missing gene | Plastidial ThMP or thiamin transporter | # plastid membrane | ThMP is synthesized in plastids [PMID:20655074]. ThMP could then be: (i) exported to cytosol and hydrolysed there to thiamin, followed by conversion to ThDP; or (ii) hydrolysed to thiamin in plastids, with thiamin being exported to cytosol. These scenarios cannot be distinguished since the location of ThMP-phosphatase activity is unknown. | No candidate genes suggested in plants. | ||||
| ThDP transp | At3g21390* | Tpc1 | Mitochondrial thiamine diphosphate transporter TPC1 | # mitochondrial membrane (experimental evidence in Arabidopsis and maize) | Mitochondrion - E [PMID:22426856] | Like other organelles, mitochondria need to import ThDP. Candidate Arabidopsis genes were predicted based on similarity to human and yeast ThDP transporters [PMID:21443630]. The two predicted Arabidopsis gene and their two maize homologs complemented the yeast TPC1 null mutant and restored the level of mitochondrial ThDP [PMID:22426856]. | |||
| ThDP transp | At5g48970* | Tpc2 | Mitochondrial thiamine diphosphate transporter TPC1 | # mitochondrial membrane (experimental evidence in Arabidopsis and maize) | Mitochondrion - E [PMID:22426856] | Like other organelles, mitochondria need to import ThDP. Candidate Arabidopsis genes were predicted based on similarity to human and yeast ThDP transporters [PMID:21443630]. The two predicted Arabidopsis gene and their two maize homologs complemented the yeast TPC1 null mutant and restored the level of mitochondrial ThDP [PMID:22426856]. | |||
| ThDP transp | GRMZM2G124911* | Mitochondrial thiamine diphosphate transporter TPC1 | # mitochondrial membrane (experimental evidence in Arabidopsis and maize) | Mitochondrion - E [PMID:22426856] | Like other organelles, mitochondria need to import ThDP. Candidate Arabidopsis genes were predicted based on similarity to human and yeast ThDP transporters [PMID:21443630]. The two predicted Arabidopsis gene and their two maize homologs complemented the yeast TPC1 null mutant and restored the level of mitochondrial ThDP [PMID:22426856]. | ||||
| ThDP transp | GRMZM2G118515* | Mitochondrial thiamine diphosphate transporter TPC1 | # mitochondrial membrane (experimental evidence in Arabidopsis and maize) | Mitochondrion - E [PMID:22426856] | Like other organelles, mitochondria need to import ThDP. Candidate Arabidopsis genes were predicted based on similarity to human and yeast ThDP transporters [PMID:21443630]. The two predicted Arabidopsis gene and their two maize homologs complemented the yeast TPC1 null mutant and restored the level of mitochondrial ThDP [PMID:22426856]. | ||||
| ThDP transp | Missing gene | Plastidial thiamine diphosphate transporter | # plastid membrane | The following considerations imply the need for import of ThDP into plastids: (i) TPPK activity, the sole mechanism to form ThDP in plants, is localized only in cytosol [PMID:17611796]; (ii) ThDP is a cofactor for plastid-localized isozymes including pyruvate dehydrogenase [PMID:13677473] and transketolase [PMID:8980496]. | No candidate genes suggested in plants. Plastidial ThDP carrier(s) are still unknown, since both TPC1-like ThDP carriers in Arabidopsis and maize are targeted to mitochondria [PMID:22426856]. | ||||
| ThDP transp | Potentially missing gene | Peroxisomal thiamine diphosphate transporter | # peroxisome membrane | Import of ThDP into plant peroxisomes is likely because, like animals [PMID:10468558], plants probably have at least one peroxisomal ThDP-dependent enzyme (2-hydroxyacyl-CoA lyase), but TPPK is strictly cytosolic in plants. | No candidate genes suggested in plants. It is not clear whether ThDP enters peroxisomes via a dedicated transporter. An alternative possibility that it enters in a bound form associated with a fully assembled enzyme, as suggested for rat liver [PMID:17596263]. | ||||
| ThDP transp | Missing gene | Plasma membrane thiamin diphosphate transporter | # plasma membrane | Rescue of Arabidopsis TPK1/TPK2 double mutant by foliar application of ThDP [PMID:17611796] implies the existence of a ThDP transporter in the plasma membrane. | No candidate genes suggested in plants. A mammalian plasma membrane transporter potentially able to transport ThDP is the reduced folate carrier SLC19A1 [PMID:11997266]. There are no clear SLC19A1 homologs in Arabidopsis. | ||||
| Transport of thiamin precursors and degradation products | |||||||||
| HMP transp | Missing gene | Transporter for 2-methyl-4-amino-5-hydroxymethylpyrimidine | # plasma membrane | Arabidopsis mutants in the pyrimidine branch of thiamin synthesis are rescued by supplied HMP e.g. [PMID:5364924]. | No candidate genes suggested in plants. | ||||
| HET transp | Missing gene | Transporter for 4-methyl-5-(2-hydroxyethyl)-thiazole | # plasma membrane | Arabidopsis mutants in the thiazole branch of thaimin synthesis are rescued by supplied HET e.g. [PMID:5364924]. | No candidate genes suggested in plants. | ||||
| HMP(P) transp | Missing gene | Transporter for 2-methyl-4-amino-5-hydroxymethylpyrimidine or its phosphate | # plastid membrane | The maize HMP(P)K/TMP-PPse enzyme phosphorylates HMP as well as HMP-P in vitro [PMID:17696876], which is consistent with the rescue of pyrimidine synthesis mutants by supplied HMP e.g. [PMID:5364924]. Plastidial localization of this enzyme points to this organelle as an HMP salvage location. | No candidate genes suggested in plants. It is unclear whether a dedicated HMP transporter exists in plant plasma or plastid membranes. In yeast this compound is apparently taken up by a common transport system with thiamin [PMID:2407290], while in Salmonella a HMP-specific transport system is believed to exist [PMID:6357279]. No sequences were identified in these studies. Several hypothetical transport systems in prokaryotes were predicted to take up HMP (or related compounds) [PMID:12376536], and thiXYZ was experimentally verified as a formyl aminopyrimidine transporter [PMID:17618314]; there are no homologs in Arabidopsis. | ||||
| HET(P) transp | Missing gene | Transporter for 4-methyl-5-(2-hydroxyethyl)-thiazole or its phosphate | # plastid membrane | Arabidopsis thiazole synthesis mutants can be rescued with thiazole e.g. [PMID:5849557] [PMID:5364924], implying the existence of HET transporters in the plastid membrane as well as the plasma membrane (see above). Since localization of hydroxyethylthiazole kinase (HET-K) activity in plants is uncertain (plastid or cytosol?), it is unknown whether HET or HET-P is imported into plastids (where HET-P can be utilized by TMP-PPse) | No candidate genes suggested in plants. HET uptake has been demonstrated in E. coli [PMID:4584810] and Salmonella [PMID:6357278]; several putative HET(P) transport systems have been predicted in prokaryotes [PMID:12376536] but have not been experimentally verified and have no homologs in Arabidopsis. | ||||
| ThDP degr.pr. | Potentially missing genes | Transporters for thiamin diphosphate degradation products | # plastid and/or mitochondrial membrane | The nature and subcellular localization of ThDP degradation pathways and products are unknown in plants [PMID:20655074], and poorly understood in other organisms. But they are likely important in ThDP metabolism, since: (i) ThDP is unstable when bound to ThDP-dependent enzymes and undergoes slow destruction during catalysis [PMID:17010220]; (ii) the pyrimidine moiety HMP-P is a toxic analog of pyridoxal phosphate, and so cannot be allowed to accumulate [PMID:13214075]; and (iii) de novo biosynthesis of thiamin is costly, an extreme example being the single-turnover enzyme Thi4 that serves as the sulfur source for thiazole synthesis [PMID:22031445]. | No candidate genes suggested in plants. It is not known whether ThDP degradation products are transported into a specific organelle (the plastid?) for salvage, or whether salvage occurs in various subcellular compartments. | ||||
| Table Notes | |||||||||
| Enzyme abbreviations (column "Abbrev") correspond to those in the thiamin pathway diagram (Fig. 2) and are defined in column "Functional role" ("Functional role"). Enzyme and transporter colour-coding is coordinated between the table and the pathway diagram and is explained at the top of the table (Legend). | |||||||||
| Arabidopsis gene IDs (column "AT gene ID") correspond to genome version AtGDB171/TAIR9 (www.plantgdb.org) (genome 3702 in the SEED database). Maize gene IDs (column "Maize ortholog") correspond to the Filtered Gene Set of the B73 cultivar genome sequence version AGPv2 (www.maizesequence.org) (genome 381124 in the SEED database). An attempt was made to establish orthology between Arabidopsis and maize genes, and the orthologous gene pairs are shown in the same rows. When one-on-one orthology could not be established, homologs appear in separate rows and are marked with an asterisk. | |||||||||
| Column "Curated localization" gives curated localizations (preceded by the # symbol) based on experimental and/or bioinformatics data for Arabidopsis, maize, or other plants; data are given specifically for Arabidopsis and maize in their respective columns. Abbreviations are: E - experimental evidence; P - predicted bioinformatically; PPDB - The Plant Proteome Database (ppdb.tc.cornell.edu). The column "Experimental data" briefly reviews experimental findings (other than enzyme localization) available for Arabidopsis, maize, or other plants. Publications are referenced by PubMed IDs (when available), which are linked to the PubMed database. The column "Problems, open questions, predictions" concerns gaps and inconsistencies in current knowledge. | |||||||||