If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
Synonyms: dihydroxyacetone cycle, xylulose-monophosphate cycle
|Superclasses:||Degradation/Utilization/Assimilation → C1 Compounds Utilization and Assimilation → Formaldehyde Assimilation|
Expected Taxonomic Range: Fungi
Methylotrophs are organisms that are capable of growing on C1 compounds, like methanol. These organisms can derive all their energy and carbon needs from reduced molecules that have no C-C bond. Methylotrophy is found only in a few prokaryotic and eukaryotic microorganisms. While prokaryotic methylotrophs are capable of growing on a variety of C1 compounds (see methane oxidation to methanol I and methanol and methylamine oxidation to formaldehyde), eukaryotic methylotrophs can grow only on methanol.
Methylotrophic eukaryotes include only a few species of yeast that belong to the Pichia and Candida genera. They include Candida boidinii, Candida methanolovescens, Candida methylica, Ogataea angusta (previously known as Hansenula polymorpha), Ogataea methanolica and Komagataella pastoris [Houard02].
In these organisms methanol is oxidized to formaldehyde by the enzyme alcohol oxidase (AOD) in a reaction that produces formaldehyde and hydrogen peroxide (see methanol oxidation to formaldehyde IV). To avoid damage to the cell by these very active compounds, this reaction occurs in peroxisomes, where catalase decomposes the hydrogen peroxide into water and oxygen [vanderKlei06].
The formaldehyde that is formed is a branchpoint, as it can be channeled into either an assimilatory pathway that provides the cells with carbon for biosynthesis (this pathway), or a dissimilatory pathway, which provides the cells with energy (see formaldehyde oxidation II (glutathione-dependent)) [vanderKlei06].
About This Pathway
Methylotrophs usually assimilate carbon by converting three C1 molecules into a single C3 compound via a cyclic pathway, similar to the Calvin-Benson-Bassham cycle used in photosynthesis. In prokaryotes, two such pathways are known, including the ribulose monophosphate cycle (formaldehyde assimilation II (RuMP Cycle)) and the serine pathway (formaldehyde assimilation I (serine pathway)). In methylotrophic yeast only one such pathway exists, the formaldehyde assimilation III (dihydroxyacetone cycle) [vanDijken78].
Three molecules of formaldehyde, generated in the peroxisome by alcohol oxidase, are processed by this pathway into a single molecule of D-glyceraldehyde 3-phosphate, which is shuttled into the core biosynthetic pathways.
The key step of this pathway is the transfer of a glycoaldehyde group from D-xylulose 5-phosphate to formaldehyde, forming dihydroxyacetone and D-glyceraldehyde 3-phosphate. This reaction is catalyzed by dihydroxyacetone synthase (DHAS), another peroxisomal enzyme [Janowicz85]. DHAS). The products of this reaction leave the peroxisome and are rearranged in the cytoplasmic in a pathway that involves many of the enzymes of the pentose phosphate pathway, in a way that regenerates D-xylulose 5-phosphate and, for every three cycles, generates one net molecule of D-glyceraldehyde 3-phosphate that is directed towards biosynthesis [vanDijken78, Anthony82].
Since the diagram does not represent this pathway with clarity, more information is provided here:
For every molecule of D-glyceraldehyde 3-phosphate that is incorporated into biomass, three molecules of formaldehyde are fixed, generating three molecules of dihydroxyacetone, and consuming three molecules of D-xylulose 5-phosphate (X5P). Two of the dihydroxyacetone molecules are condensed with two molecules of D-glyceraldehyde 3-phosphate to produce two molecules of fructose 1,6-bisphosphate, while the third one is converted to D-glyceraldehyde 3-phosphate, 1,3-bisphospho-D-glycerate and finally 3-phospho-D-glycerate, and routed to biosynthesis.
Each of the three molecules of X5P that are utilized is regenerated in a different route. First, the two molecules of fructose 1,6-bisphosphate mention above are dephosphorylated into two molecules of β-D-fructofuranose 6-phosphate by the enzyme EC 22.214.171.124. One molecule of X5P is regenerated directly from β-D-fructofuranose 6-phosphate by EC 126.96.36.199, in a reaction that also generates a molecule of D-erythrose 4-phosphate. The second X5P molecule is generated from the other β-D-fructofuranose 6-phosphate molecule in a different route, consuming the D-erythrose 4-phosphate and generating D-sedoheptulose 7-phosphate (catalyzed by EC 188.8.131.52), which is then converted to X5P by EC 184.108.40.206, in a reaction that also generates D-ribose 5-phosphate. Finally, the D-ribose 5-phosphate molecule is converted to D-ribulose 5-phosphate by EC 220.127.116.11, which is then converted to the third X5P molecule by EC 18.104.22.168 [Anthony82].
Houard02: Houard S, Heinderyckx M, Bollen A (2002). "Engineering of non-conventional yeasts for efficient synthesis of macromolecules: the methylotrophic genera." Biochimie 84(11);1089-93. PMID: 12595136
Janowicz85: Janowicz ZA, Eckart MR, Drewke C, Roggenkamp RO, Hollenberg CP, Maat J, Ledeboer AM, Visser C, Verrips CT (1985). "Cloning and characterization of the DAS gene encoding the major methanol assimilatory enzyme from the methylotrophic yeast Hansenula polymorpha." Nucleic Acids Res 13(9);3043-62. PMID: 2987872
vanderKlei06: van der Klei IJ, Yurimoto H, Sakai Y, Veenhuis M (2006). "The significance of peroxisomes in methanol metabolism in methylotrophic yeast." Biochim Biophys Acta 1763(12);1453-62. PMID: 17023065
Alvarez98: Alvarez M, Zeelen JP, Mainfroid V, Rentier-Delrue F, Martial JA, Wyns L, Wierenga RK, Maes D (1998). "Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties." J Biol Chem 273(4);2199-206. PMID: 9442062
Baldwin78: Baldwin SA, Perham RN (1978). "Novel kinetic and structural properties of the class-I D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes' strain)." Biochem J 1978;169(3);643-52. PMID: 348198
Baldwin78a: Baldwin SA, Perham RN, Stribling D (1978). "Purification and characterization of the class-II D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes' strain)." Biochem J 1978;169(3);633-41. PMID: 417719
Beaucamp97: Beaucamp N, Hofmann A, Kellerer B, Jaenicke R (1997). "Dissection of the gene of the bifunctional PGK-TIM fusion protein from the hyperthermophilic bacterium Thermotoga maritima: design and characterization of the separate triosephosphate isomerase." Protein Sci 1997;6(10);2159-65. PMID: 9336838
Beaucamp97a: Beaucamp N, Schurig H, Jaenicke R (1997). "The PGK-TIM fusion protein from Thermotoga maritima and its constituent parts are intrinsically stable and fold independently." Biol Chem 1997;378(7);679-85. PMID: 9278147
Berthiaume89: Berthiaume L, Beaudry D, Lazure C, Tolan DR, Sygusch J (1989). "Recombinant anaerobic maize aldolase: overexpression, characterization, and metabolic implications." Arch Biochem Biophys 272(2);281-9. PMID: 2751305
Branny98: Branny P, de la Torre F, Garel JR (1998). "An operon encoding three glycolytic enzymes in Lactobacillus delbrueckii subsp. bulgaricus: glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and triosephosphate isomerase." Microbiology 144 ( Pt 4);905-14. PMID: 9579064
Brown09: Brown G, Singer A, Lunin VV, Proudfoot M, Skarina T, Flick R, Kochinyan S, Sanishvili R, Joachimiak A, Edwards AM, Savchenko A, Yakunin AF (2009). "Structural and biochemical characterization of the type II fructose-1,6-bisphosphatase GlpX from Escherichia coli." J Biol Chem 284(6);3784-92. PMID: 19073594
Bystrykh83: Bystrykh LV, Trotsenko IuA (1983). "[Purification and several properties of dihydroxyacetone kinase from the methylotrophic yeast Candida boidinii]." Biokhimiia 48(10);1611-6. PMID: 6315084
Cabezas05: Cabezas A, Costas MJ, Pinto RM, Couto A, Cameselle JC (2005). "Identification of human and rat FAD-AMP lyase (cyclic FMN forming) as ATP-dependent dihydroxyacetone kinases." Biochem Biophys Res Commun 338(4);1682-9. PMID: 16289032
Cancilla95: Cancilla MR, Davidson BE, Hillier AJ, Nguyen NY, Thompson J (1995). "The Lactococcus lactis triosephosphate isomerase gene, tpi, is monocistronic." Microbiology 141 ( Pt 1);229-38. PMID: 7534588
Chaikuad11: Chaikuad A, Shafqat N, Al-Mokhtar R, Cameron G, Clarke AR, Brady RL, Oppermann U, Frayne J, Yue WW (2011). "Structure and kinetic characterization of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase, GAPDS." Biochem J 435(2);401-9. PMID: 21269272
Showing only 20 references. To show more, press the button "Show all references".
©2015 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493