MetaCyc Chimeric Pathway: superpathway of seleno-compound metabolism
Author statementInferred from experiment

Pathway diagram: superpathway of seleno-compound metabolism

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: superpathway of seleno-compound detoxification, superpathway of selenium uptake and metabolism, superpathway of seleno-amino acid biosynthesis and detoxification

Superclasses: BiosynthesisAmino Acids BiosynthesisOther Amino Acid Biosynthesis
Degradation/Utilization/AssimilationInorganic Nutrients MetabolismSelenium MetabolismSeleno-Amino Acid Detoxification
DetoxificationSeleno-Amino Acid Detoxification

Some taxa known to possess parts of the pathway include : Arabidopsis thaliana col, Astragalus, Astragalus bisulcatus, Brassica juncea, Brassica oleracea capitata, Brassica oleracea italica, Neptunia, Pisum sativum, Saccharomyces cerevisiae, Spartina, Spinacia oleracea, Sporobolus alterniflorus

Expected Taxonomic Range: Bacteria , Fungi, Viridiplantae

Note: This is a chimeric pathway, comprising reactions from multiple organisms, and typically will not occur in its entirety in a single organism. The taxa listed here are likely to catalyze only subsets of the reactions depicted in this pathway.

General Background

Selenium is an essential micronutrient for animals and humans but has not yet been proven to be an essential micronutrient for land plants [Brown01c, Sors05a]. There is evidence, however, of Chlamydomonas proteins that contains a L-selenocysteine residue suggesting that algal species might also require Se0 [Kim06m, Novoselov02]. The health requirement of Se0 for humans and animals can be met by crops and forage plants that contain selenocompounds. Helianthus annuus among the oilseed crops was shown to be a good source for this micronutrient [Terry00]. In addition, there is evidence that certain seleno-compounds, including seleno-L-methionine, have anti-carcinogenic properties [Whanger04].

Despite its importance as a micronutrient, higher concentrations of Se0 are toxic to humans, other animals, and plants largely because transporters and enzymes involved in sulfur and sulfo-compound metabolism can often erroneously substitute Se0 for sulfur and can misincorporate seleno-amino acids into proteins [Zwolak11, Ellis03, Brown81a].

In general, plants take up both selenate and selenite from soil. A series of reduction steps converts selenate to selenide / hydrogen selenide and this is assimilated into the seleno-amino acids L-selenocysteine and seleno-L-methionine [Sors09].

In Se accumulator plants, these seleno-amino acids may be modified to create organic seleno-compounds for storage. Seasonal weeds like Silene gallica and Avena sterilis ludoviciana along with perennial weeds like Cirsium arvense employ this strategy and accumulate high amounts of Se0 [Dhillon09]. Se accumulation can help to protect plants against attacks by prairie dogs, insects, and fungi (see refs in [Freeman09]).

Other plants, like Arabidopsis thaliana col generate seleno-compounds as well, but rather than storing them, they transform them into less toxic volatile compounds such as dimethyl selenide (DMSe) that can then be released from the plants [deSouza00]. This process is also called phytovolatilization [Zhou09a].

While these strategies directly benefit the plants that employ them, they can also be put to use for the phytoremediation of seleniferous soils that contain dangerously high amounts of Se0. Numerous insights into endogenous seleno-compound metabolism in plants have been gained through efforts to engineer plants that show improved selenium phytoremediation abilities [Ellis04, Dhillon09, Zhou10, Banuelos07, deSouza00].

About This Pathway

In many plant species the metabolism of selenium appears to mirror the metabolism of sulfur and often uses the same enzymes. Therefore, although this pathway has not been completely elucidated in plants, it has been built based on the comparable sulfur-based pathways, such as the reductive sulfur assimilation pathway found in plants [Sors05a].

As in the sulfur reduction pathway, the ATP sulfurylase enzyme appears to catalyze the first step in selenium reduction. This claim is supported by the finding that overexpression of an Arabiopsis ATP sulfurylase promotes selenate reduction [PilonSmits99, Sors05].

The second step in the pathway is still being investigated. There is evidence for non-enzymatic conversion of to selenite in vitro [Dilworth77], but selenite reductase activity has been observed in planta and has been measured in a number of selenium hyperaccumulators [Sors05].

To date, there is no evidence that a sulfite reductase enzyme is needed to catalyze the third reaction in the pathway in plants. Rather, evidence collected using pea chloroplasts suggests that this reaction can proceed non-enzymatically and uses both glutathione and NADPH as reducing agents [Jablonski82].

Analyses of the overall reduction of selenate to organic selenium suggest that the first step of selenate reduction is rate-limiting [deSouza98].

This portion of the pathway is believed to occur in the choloroplast [Ellis03].

Similar to the selenate reduction portion of the pathway, selenocysteine formation likely parallels the cysteine biosynthetic pathway in plants, and may use many of the same enzymes.The first step in cysteine biosynthesis involes a serine acetyltransferase (SAT). While there is definite evidence of enzymes capable of producing O-acetyl-L-serine in Arabidopsis and many other plant species, these enzymes have not yet been explicitly linked to selenium metabolism in planta. In fact, when SAT activity is compared across different Astragalus species that accumulate vastly different levels of selenium, no correlation is detected [Sors05]. Selenocysteine formation is likely to be catalyzed by O-acetyl-L-serine (thiol) lyase (OAS-TL) enzymes and selenocysteine production in the presence of O-acteyl-serine has been measured in a number of plants including including Pisum sativum (pea), clover, and several Astralagus species [Ng78]. This activity could be competitively inhibited by sulfur, and conversely, cysteine biosynthesis could be competetively inhibited by selenium, arguing that these reactions are catalyzed by the same enzymes [Ng78]. Direct evidence for OAS-TL-based production of selenocysteine has only been demonstrated in the bacteria Paracoccus denitrificans to date [Burnell77], but it is likely that plant OAS-TLs catalyze this reaction, too.

L-selenocystathionine production probably depends on the activity of the cystathionine synthase enzymes that play a comparable role in sulfate metabolism. Over-expression of an Arabidopsis CGS1 enzyme in Brassica juncea appears to increase flux through this pathway and leads to higher levels of volatile selenium compound production [Van03].

Evidence for activity of the next enzyme in the pathway, β-(seleno)cystathionine lyase can be detected in plant extracts from several species including selenium non-accumulators, such as spinach (see L-cystathione β-lyase / β L-selenocystathionase ), pea and Se accumulators, such as Astragalus bisulcatus. As seen for many other enzymes in this pathway, it is active with both the sulfur and selenium analogs [McCluskey86].

The final step toward selenomethionine biosynthesis could be catalyzed by at least three different types of enzymes if the proteins involved in L-methionine biosynthesis II also participate in selenomethionine (Se-Met) metabolism. For instance, E.coli has both cobalamin-dependent ( and cobalamin-independent enzymes ( that can catalyze the formation of Se-Met [Zhou00]. No cobalamin-independent candidates have been found in Arabidopsis. On the other hand, it does have three cobalamin-independent methionine synthases (see 2.1.14) which could also potentially accept selenohomocysteine, but their role in seleno-amino acid biosynthesis has not yet been tested [Ravanel04].

Both seleno-amino acids, L-selenocysteine and seleno-L-methionine, can be misincorporated during protein synthesis. To prevent this, selenium accumulating or hyperaccumulating plants typically transform them into non-coding seleno-amino acids, such as Se-methylselenocysteine or other related compounds. Non-accumulating plants employ a different strategy and further metabolize these seleno-amino acids into the production of volatile compounds that can be released into the atmosphere [Sors05a]. Several different routes for seleno-amino acid detoxification are incorporated into this superpathway and it is unlikely that any one species employs all of them. In particular, within the plant kingdom, seleno-amino acid detoxification and volatilization II via dimethylselenoniopropanoate production, may be limited to halophytic species.

Two sub-pathways describe alternative routes that Se-non-accumulating and accumulating plants may use to further metabolize seleno-L-methionine to produce the volatile dimethyl selenide. In the hyperaccumulator Spartina species, this may occur in a four-step process that involves the formation of the intermediate compound 3-dimethylselenopropionaldehyde. The Spartina enzymes shown to function in DMSP biosynthesis [Kocsis00] may perform analogous functions in DMSeP production. However, this intermediate is not likely produced in Arabidopsis and many other plants. Therefore, a one-step variant has been proposed. Formation of dimethyl selenide may be catalyzed by a putative methylmethionine / Se-methyl-Se-methionine hydrolase in Arabidopsis thaliana and other plants, but no such enzyme has been identified or characterized yet, particularly with respect to seleno-compound metabolism [Tagmount02]. It is also possible that this reaction may happen spontaneously through chemical decomposition, but this would be expected to occur very slowly at physiological pH.

Roots may be the primary site of dimethyl selenide production (see citations in [deSouza98]).

Only one sub-pathway describing the further metabolism of L-selenocysteine has been suggested so far, and it lacks some important details concerning the final steps of dimethyl diselenide production. It is possible that a series of reactions involving first a selenium methylselenocysteine selenoxide intermediate and then a methaneseleniol intermediate are required, similar to the enzymatic steps observed for dimethyldisulfide biosynthesis [Sors05a].

It is also possible that some of the L-selenocysteine can be shunted toward dimethyl selenide production if enzymes such as the bacterial thiopurine methyltransferase are found to occur in plants [Ranjard02, Sors05a].

Selenocysteine may also be used to form γ-L-glutamyl-Se-methyl-L-selenocysteine as this compound has been seen to accumulate in Arabidopsis over-expressing a selenocysteine methyltransferase enzyme and natively, in the hyperaccumulator Astragalus bisulcatus [Nigam69, Nigam69a, Sors05a].

Subpathways: seleno-amino acid detoxification and volatilization I, seleno-amino acid biosynthesis, selenate reduction, seleno-amino acid detoxification and volatilization III, seleno-amino acid detoxification and volatilization II

Unification Links: PlantCyc:PWY-6395

Created 01-Dec-2009 by Pujar A, Boyce Thompson Institute
Revised 21-Oct-2011 by Dreher KA, PMN


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Burnell77: Burnell JN, Whatley FR (1977). "Sulphur metabolism in Paracoccus denitrificans. Purification, properties and regulation of serine transacetylase, O-acetylserine sulphydrylase and beta-cystathionase." Biochim Biophys Acta 481(1);246-65. PMID: 14692

Burnell81: Burnell JN (1981). "Selenium Metabolism in Neptunia amplexicaulis." Plant Physiol 67(2);316-24. PMID: 16661667

deSouza00: de Souza MP, Lytle CM, Mulholland MM, Otte ML, Terry N (2000). "Selenium assimilation and volatilization from dimethylselenoniopropionate by Indian mustard." Plant Physiol 122(4);1281-8. PMID: 10759525

deSouza98: de Souza MP , Pilon-Smits EA, Lytle CM, Hwang S, Tai J, Honma TS, Yeh L, Terry N (1998). "Rate-limiting steps in selenium assimilation and volatilization by indian mustard." Plant Physiol 117(4);1487-94. PMID: 9701603

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Ellis04: Ellis DR, Sors TG, Brunk DG, Albrecht C, Orser C, Lahner B, Wood KV, Harris HH, Pickering IJ, Salt DE (2004). "Production of Se-methylselenocysteine in transgenic plants expressing selenocysteine methyltransferase." BMC Plant Biol 4;1. PMID: 15005814

Freeman09: Freeman JL, Quinn CF, Lindblom SD, Klamper EM, Pilon-Smits EA (2009). "Selenium protects the hyperaccumulator Stanleya pinnata against black-tailed prairie dog herbivory in native seleniferous habitats." Am J Bot 96(6);1075-85. PMID: 21628258

Jablonski82: Jablonski, P., Anderson, J. (1982). "Light-dependent reduction of selenite by sonicated pea chloroplasts." Phytochemistry. 21(9): 2179-2184.

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McCluskey86: McCluskey, T.J., Scarf, A.R., Anderson, J.W. (1986). "Enzyme catalysed α,β-elimination of selenocystathionine and selenocystine and their sulphur isologues by plant extracts." Phytochemistry. 25(9): 2063-2068.

Ng78: Ng, B.H., Anderson, J.W. (1978). "Synthesis of selenocysteine by cysteine synthases from selenium accumulator and non-accumulator plants." Phytochemistry. 17(12):2069-2074.

Nigam69: Nigam, S.N., McConnell. W.B. (1969). "Distribution of selenomethylselenocysteine and some other amino acids in species of Astragalus, with special reference to their distribution during the growth of A. bisulcatus." Phytochemistry. 8(7):1161-1165.

Nigam69a: Nigam SN, McConnell WB (1969). "Seleno amino compounds from Astragalus bisculcatus. Isolation and identification of gamma-L-glutamyl-Se-methyl-seleno-L-cysteine and Se-methylseleno-L-cysteine." Biochim Biophys Acta 192(2);185-90. PMID: 5370015

Novoselov02: Novoselov SV, Rao M, Onoshko NV, Zhi H, Kryukov GV, Xiang Y, Weeks DP, Hatfield DL, Gladyshev VN (2002). "Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii." EMBO J 21(14);3681-93. PMID: 12110581

PilonSmits99: Pilon-Smits EA, Hwang S, Mel Lytle C , Zhu Y, Tai JC, Bravo RC, Chen Y, Leustek T, Terry N (1999). "Overexpression of ATP sulfurylase in indian mustard leads to increased selenate uptake, reduction, and tolerance." Plant Physiol 119(1);123-32. PMID: 9880353

Ranjard02: Ranjard L, Prigent-Combaret C, Nazaret S, Cournoyer B (2002). "Methylation of inorganic and organic selenium by the bacterial thiopurine methyltransferase." J Bacteriol 184(11);3146-9. PMID: 12003960

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Sors05: Sors TG, Ellis DR, Na GN, Lahner B, Lee S, Leustek T, Pickering IJ, Salt DE (2005). "Analysis of sulfur and selenium assimilation in Astragalus plants with varying capacities to accumulate selenium." Plant J 42(6);785-97. PMID: 15941393

Sors05a: Sors TG, Ellis DR, Salt DE (2005). "Selenium uptake, translocation, assimilation and metabolic fate in plants." Photosynth Res 86(3);373-89. PMID: 16307305

Sors09: Sors TG, Martin CP, Salt DE (2009). "Characterization of selenocysteine methyltransferases from Astragalus species with contrasting selenium accumulation capacity." Plant J 59(1);110-22. PMID: 19309459

Tagmount02: Tagmount A, Berken A, Terry N (2002). "An essential role of s-adenosyl-L-methionine:L-methionine s-methyltransferase in selenium volatilization by plants. Methylation of selenomethionine to selenium-methyl-L-selenium- methionine, the precursor of volatile selenium." Plant Physiol 130(2);847-56. PMID: 12376649

Terry00: Terry N, Zayed AM, De Souza MP, Tarun AS (2000). "SELENIUM IN HIGHER PLANTS." Annu Rev Plant Physiol Plant Mol Biol 51;401-432. PMID: 15012198

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Whanger04: Whanger PD (2004). "Selenium and its relationship to cancer: an update." Br J Nutr 91(1);11-28. PMID: 14748935

Zhou00: Zhou ZS, Smith AE, Matthews RG (2000). "L-Selenohomocysteine: one-step synthesis from L-selenomethionine and kinetic analysis as substrate for methionine synthases." Bioorg Med Chem Lett 10(21);2471-5. PMID: 11078203

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Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Ansede97: Ansede, J.H., Yoch, D.C. (1997). "Comparison of selenium and sulfur volatilization by dimethylsulfoniopropionate lyase (DMSP) in two marine bacteria and estuarine sedimentsAnsede, J.H.; Yoch, D.C.; . 23, 315-324 (1997)." FEMS Microbiology Ecology. 23(4): 315-324.

Barkes76: Barkes L, Fleming RW (1976). "Effects of alternative selenium and sulfur sources on dimethylselenide production by two fungi isolated from natural systems." Bull Environ Contam Toxicol 15(4);504-8. PMID: 1260159

Berkowitz02: Berkowitz O, Wirtz M, Wolf A, Kuhlmann J, Hell R (2002). "Use of biomolecular interaction analysis to elucidate the regulatory mechanism of the cysteine synthase complex from Arabidopsis thaliana." J Biol Chem 277(34);30629-34. PMID: 12063244

Bick98: Bick JA, Aslund F, Chen Y, Leustek T (1998). "Glutaredoxin function for the carboxyl-terminal domain of the plant-type 5'-adenylylsulfate reductase." Proc Natl Acad Sci U S A 1998;95(14);8404-9. PMID: 9653199

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Droux98: Droux M, Ruffet ML, Douce R, Job D (1998). "Interactions between serine acetyltransferase and O-acetylserine (thiol) lyase in higher plants--structural and kinetic properties of the free and bound enzymes." Eur J Biochem 1998;255(1);235-45. PMID: 9692924

Hindson03: Hindson VJ, Shaw WV (2003). "Random-order ternary complex reaction mechanism of serine acetyltransferase from Escherichia coli." Biochemistry 42(10);3113-9. PMID: 12627979

Howarth97: Howarth JR, Roberts MA, Wray JL (1997). "Cysteine biosynthesis in higher plants: a new member of the Arabidopsis thaliana serine acetyltransferase small gene-family obtained by functional complementation of an Escherichia coli cysteine auxotroph." Biochim Biophys Acta 1997;1350(2);123-7. PMID: 9048879

Hsieh75: Hsieh HS, Ganther HE (1975). "Acid-volatile selenium formation catalyzed by glutathione reductase." Biochemistry 14(8);1632-6. PMID: 235962

Kocsis03: Kocsis MG, Ranocha P, Gage DA, Simon ES, Rhodes D, Peel GJ, Mellema S, Saito K, Awazuhara M, Li C, Meeley RB, Tarczynski MC, Wagner C, Hanson AD (2003). "Insertional inactivation of the methionine s-methyltransferase gene eliminates the s-methylmethionine cycle and increases the methylation ratio." Plant Physiol 131(4);1808-15. PMID: 12692340

Kredich66: Kredich NM, Tomkins GM (1966). "The enzymic synthesis of L-cysteine in Escherichia coli and Salmonella typhimurium." J Biol Chem 1966;241(21);4955-65. PMID: 5332668

Kumagai10: Kumagai T, Koyama Y, Oda K, Noda M, Matoba Y, Sugiyama M (2010). "Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae." Antimicrob Agents Chemother 54(3);1132-9. PMID: 20086163

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

LeDuc04: LeDuc DL, Tarun AS, Montes-Bayon M, Meija J, Malit MF, Wu CP, AbdelSamie M, Chiang CY, Tagmount A, deSouza M, Neuhierl B, Bock A, Caruso J, Terry N (2004). "Overexpression of selenocysteine methyltransferase in Arabidopsis and Indian mustard increases selenium tolerance and accumulation." Plant Physiol 135(1);377-83. PMID: 14671009

LeDuc06: LeDuc DL, AbdelSamie M, Montes-Bayon M, Wu CP, Reisinger SJ, Terry N (2006). "Overexpressing both ATP sulfurylase and selenocysteine methyltransferase enhances selenium phytoremediation traits in Indian mustard." Environ Pollut 144(1);70-6. PMID: 16515825

Leustek94: Leustek T, Murillo M, Cervantes M (1994). "Cloning of a cDNA encoding ATP sulfurylase from Arabidopsis thaliana by functional expression in Saccharomyces cerevisiae." Plant Physiol 1994;105(3);897-902. PMID: 8058839

Lyi05: Lyi SM, Heller LI, Rutzke M, Welch RM, Kochian LV, Li L (2005). "Molecular and biochemical characterization of the selenocysteine Se-methyltransferase gene and Se-methylselenocysteine synthesis in broccoli." Plant Physiol 138(1);409-20. PMID: 15863700

Meija02: Meija J, Montes-Bayon M, Le Duc DL, Terry N, Caruso JA (2002). "Simultaneous monitoring of volatile selenium and sulfur species from se accumulating plants (wild type and genetically modified) by GC/MS and GC/ICPMS using solid-phase microextraction for sample introduction." Anal Chem 74(22);5837-44. PMID: 12463370

Murillo95a: Murillo M, Foglia R, Diller A, Lee S, Leustek T (1995). "Serine acetyltransferase from Arabidopsis thaliana can functionally complement the cysteine requirement of a cysE mutant strain of Escherichia coli." Cell Mol Biol Res 1995;41(5);425-33. PMID: 8867790

Neuhierl96: Neuhierl B, Bock A (1996). "On the mechanism of selenium tolerance in selenium-accumulating plants. Purification and characterization of a specific selenocysteine methyltransferase from cultured cells of Astragalus bisculatus." Eur J Biochem 239(1);235-8. PMID: 8706715

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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