MetaCyc Pathway: sulfite oxidation II

Enzyme View:

Pathway diagram: sulfite oxidation II

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/Assimilation Inorganic Nutrients Metabolism Sulfur Compounds Metabolism Sulfite Oxidation

Some taxa known to possess this pathway include ? : Thiobacillus denitrificans , Thiobacillus thioparus , Thiocapsa roseopersicina

Expected Taxonomic Range: Bacteria

General Background

Sulfite plays a key role in oxidative sulfur metabolism. It can derived from multiple sources: first, sulfite is the main intermediate in the oxidation of sulfur compounds to sulfate [Kappler01]. In purple sulfur bacteria such as Allochromatium vinosum, the oxidation of hydrogen sulfide and thiosulfate results in formation of intracellular sulfur globules, which are oxidized to sulfite by the Dsr system (see superpathway of sulfide oxidation (phototrophic sulfur bacteria)).

A second source for sulfite is the desulfonation of organic compounds by enzymes like EC, sulfoacetaldehyde acetyltransferase (Xsc) (see sulfoacetaldehyde degradation I).

A third source is extracellular sulfite retrieved from the environment. Free sulfite in the periplasm (which most likely exists as hydrogen sulfite) is bound to the SoxYZ protein complex in the form of [a SoxY protein]-L-cysteine-S-sulfinate. The binding acts to shield components of the periplasm from chemical reactions with sulfite, and may also be required for delivering the sulfite to a transporter that exports it into the cytoplasm for oxidation [Dahl13]. Some microorganisms (such as Sulfitobacter species) can use sulfite as their sole electron source [Sorokin95, Pukall99].

Enzymes that catalyze the direct oxidation of sulfite to sulfate are molybdenum hydroxylases, and belong to the sulfite oxidase family, which includes both sulfite-oxidizing enzymes and plant assimilatory nitrate reductases (such as the sulfite oxidase of Arabidopsis thaliana col). The best characterized members of this family are sulfite oxidases from avian and mammalian sources. However, these enzymes differ from the bacterial enzymes in that they can use oxygen as an electron acceptor (see EC, sulfite oxidase).

Some sulfite oxidizing enzyme are located in the periplasm. The best characterized enzyme from this group is sulfite dehydrogenase (SOR) from Starkeya novella, which contains a molybdopyranopterin cofactor (see sulfite oxidation I (sulfite oxidoreductase)). Another well-characterized periplasmic enzyme is the Sox enzyme system (such as that from Paracoccus pantotrophus). It has been shown that this system can oxidize sulfite in vitro, but it is not clear whether it functions in vivo as a sulfite-oxidizing enzyme [Friedrich00, Lu84, Friedrich01a]).

Other enzyme systems that oxidize sulfite are located in the cytoplasm. Two general mechanisms for sulfite oxidation in the cytoplasm have been described: a direct oxidation by a membrane-bound iron-sulfur molybdoprotein (this pathway) and an indirect, AMP-dependent oxidation via the intermediate adenosine 5'-phosphosulfate (APS) (see sulfite oxidation II and sulfite oxidation III) [Kappler01]. The direct oxidation route is much more prevalent, but the two mechanisms are present simultaneously in many organisms, including β and γ proteobacteria (Thiobacillus thioparus, Allochromatium vinosum, Thiobacillus denitrificans, Beggiatoa), green sulfur bacteria (Chlorobium), Gram-positive bacteria (Sulfobacillus thermosulfidooxidans) and even archaea (Acidianus ambivalens) [Kappler01].

While many organisms possess only the direct mechanism, the only examples for organisms that possess only the non-direct mechanism are found in the bacterial endosymbionts of invertebrates [Nelson95].

About This Pathway

Two variations are known for the non-direct sulfite oxidation pathway. Both variations share the same first step, the AMP-dependent oxidation of sulfite to adenosine 5'-phosphosulfate, which is catalyzed by the enzyme APS reductase. The pathways differ in the second step. In one variation the AMP moiety of APS is transferred to diphosphate by dissimilatory sulfate adenylyltransferase, generating sulfate and ATP (see sulfite oxidation III), while in the other variation (this pathway) the AMP-moiety is transfered to phosphate by the enzyme adenylylsulfate:phosphate adenylyltransferase (APAT), generating sulfate and ADP. The APS pathways can operate in both directions (see sulfate reduction IV (dissimilatory)), and were discovered originally in sulfate-reducing organisms [Peck62]. When operating in sulfite oxidation mode, they result in substrate level phosphorylation, and may provide the bacteria with energy [Peck68].

The oxidation of sulfite by the indirect pathways occurs in the cytoplasm. The first enzyme of both pathway, APS reductase, has been described as either a soluble enzyme, or a membrane bound enzyme. The other enzymes are soluble [Kappler01]. This pathway has been demonstrated in several organisms, including Thiocapsa roseopersicina [Alguero88], Thiobacillus thioparus and Thiobacillus denitrificans [Bruser00]. However, all of these organisms also contain the enzyme dissimilatory sulfate adenylyltransferase, suggesting the two variations of indirect sulfite oxidation co-exist in these organisms.

Superpathways: superpathway of sulfur oxidation (Acidianus ambivalens)

Variants: sulfite oxidation I (sulfite oxidoreductase) , sulfite oxidation III , sulfite oxidation IV , sulfite oxidation V (SoeABC) , superpathway of sulfur metabolism (Desulfocapsa sulfoexigens) , superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans)

Created 09-Aug-2006 by Caspi R , SRI International


Alguero88: Alguero M, Dahl C, Truper HG (1988). "Partial purification and characterization of ADP sulfurylase from the purple sulfur bacterium Thiocapsa roseopersicina." Microbiologia 4(3);149-60. PMID: 2855979

Bagchi05: Bagchi A, Ghosh TC (2005). "A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon." Biochem Biophys Res Commun 335(2);609-15. PMID: 16084835

Bruser00: Bruser T, Selmer T, Dahl C (2000). ""ADP sulfurylase" from Thiobacillus denitrificans is an adenylylsulfate:phosphate adenylyltransferase and belongs to a new family of nucleotidyltransferases." J Biol Chem 275(3);1691-8. PMID: 10636864

Dahl13: Dahl C, Franz B, Hensen D, Kesselheim A, Zigann R (2013). "Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process." Microbiology 159(Pt 12);2626-38. PMID: 24030319

Friedrich00: Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, Kostka S, Prinz H (2000). "Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17." J Bacteriol 182(17);4677-87. PMID: 10940005

Friedrich01a: Friedrich CG, Rother D, Bardischewsky F, Quentmeier A, Fischer J (2001). "Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism?." Appl Environ Microbiol 67(7);2873-82. PMID: 11425697

Kappler01: Kappler U, Dahl C (2001). "Enzymology and molecular biology of prokaryotic sulfite oxidation." FEMS Microbiol Lett 203(1);1-9. PMID: 11557133

Lu84: Lu, W.P., Kelly, D.P. (1984). "Properties and role of sulphite:cytochrome c oxidoreductase purified from Thiobacillus versutus (A2)." J. Gen. Microbiol. 130(7):1683-1692.

Nelson95: Nelson, D.C., Hagen, K.D. (1995). "Physiology and biochemistry of symbiotic and free-living chemoautotrophic sulfur bacteria." Am. Zool. 35: 91-101.

Peck62: Peck, H.D. (1962). "Symposium on metabolism of inorganic compounds. V. Comparative metabolism of inorganic sulfur compounds in microorganisms." Bacteriol Rev 26;67-94. PMID: 14484819

Peck68: Peck HD (1968). "Energy-coupling mechanisms in chemolithotrophic bacteria." Annu Rev Microbiol 22;489-518. PMID: 4972376

Pukall99: Pukall R, Buntefuss D, Fruhling A, Rohde M, Kroppenstedt RM, Burghardt J, Lebaron P, Bernard L, Stackebrandt E (1999). "Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the alpha-Proteobacteria." Int J Syst Bacteriol 49 Pt 2;513-9. PMID: 10319472

Quentmeier01: Quentmeier A, Friedrich CG (2001). "The cysteine residue of the SoxY protein as the active site of protein-bound sulfur oxidation of Paracoccus pantotrophus GB17." FEBS Lett 503(2-3);168-72. PMID: 11513876

Quentmeier03: Quentmeier A, Hellwig P, Bardischewsky F, Grelle G, Kraft R, Friedrich CG (2003). "Sulfur oxidation in Paracoccus pantotrophus: interaction of the sulfur-binding protein SoxYZ with the dimanganese SoxB protein." Biochem Biophys Res Commun 312(4);1011-8. PMID: 14651972

Sorokin95: Sorokin, D.Y. (1995). "Sulfitobacter pontiacus gen. nov., sp. nov. - a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation." Mikrobiologiya 64:354-365.

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

Dahl01: Dahl C, Truper HG (2001). "Sulfite reductase and APS reductase from Archaeoglobus fulgidus." Methods Enzymol 331;427-41. PMID: 11265481

Frederiksen03: Frederiksen TM, Finster K (2003). "Sulfite-oxido-reductase is involved in the oxidation of sulfite in Desulfocapsa sulfoexigens during disproportionation of thiosulfate and elemental sulfur." Biodegradation 14(3);189-98. PMID: 12889609

Fritz00: Fritz G, Buchert T, Huber H, Stetter KO, Kroneck PM (2000). "Adenylylsulfate reductases from archaea and bacteria are 1:1 alphabeta-heterodimeric iron-sulfur flavoenzymes--high similarity of molecular properties emphasizes their central role in sulfur metabolism." FEBS Lett 473(1);63-6. PMID: 10802060

Fritz02: Fritz G, Roth A, Schiffer A, Buchert T, Bourenkov G, Bartunik HD, Huber H, Stetter KO, Kroneck PM, Ermler U (2002). "Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution." Proc Natl Acad Sci U S A 99(4);1836-41. PMID: 11842205

Guranowski10: Guranowski A, Wojdyla AM, Zimny J, Wypijewska A, Kowalska J, Jemielity J, Davis RE, Bieganowski P (2010). "Dual activity of certain HIT-proteins: A. thaliana Hint4 and C. elegans DcpS act on adenosine 5'-phosphosulfate as hydrolases (forming AMP) and as phosphorylases (forming ADP)." FEBS Lett 584(1);93-8. PMID: 19896942

Kraemer89: Kraemer, M., Cypionka, H. (1989). "Sulfate formation via ATP sulfurylase in thiosulfate- and sulfite-disproportionating bacteria." Arch. Microbiol. 151:232-237.

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

Sanchez01: Sanchez O, Ferrera I, Dahl C, Mas J (2001). "In vivo role of adenosine-5'-phosphosulfate reductase in the purple sulfur bacterium Allochromatium vinosum." Arch Microbiol 176(4);301-5. PMID: 11685375

Zimmermann99: Zimmermann P, Laska S, Kletzin A (1999). "Two modes of sulfite oxidation in the extremely thermophilic and acidophilic archaeon acidianus ambivalens." Arch Microbiol 172(2);76-82. PMID: 10415168

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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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