Jump to content

User:CodeSwitch/sandbox

From Wikipedia, the free encyclopedia
< User:CodeSwitch
This is an old revision of this page, as edited by CodeSwitch (talk | contribs) at 03:57, 14 November 2017 (→Metabolism). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

Original: "Methylotroph"

General microbiology

Methylotrophs are a diverse group, including both Gram-negative and Gram-positive genera. None of them make resting structures like exospores or cysts and none of them have the complex intracellular membrane systems that characterize methanotrophs growing on methane

There are two sub groups:

  1. obligate methylotrophs.
  2. facultative methylotrophs.
Obligate methylotrophs

A single obligate methylotroph (methylophilus) is known. It is Gram-negative, polarly flagellated rod capable of rapid growth with methanol. Some strains can also utilize formaldehyde or methylamines. Carbon is assimilated via the ribulose mono phosphate pathway.

Facultative methylotrophs

It is relatively widely distributed trait among heterotrophic bacteria. It may also be common among chemoautotrophs: several thiobacilli and nitrifying bacteria can drive CO2 assimilation via the Calvin-Benson cycle by formate oxidation.

Edit: "Methylotroph"

Metabolism

The key intermediate behind methylotrophic metabolism is formaldehyde which can be diverted to either catabolism or anabolism.[1] Methylotrophs arrive at formaldehyde through oxidation of methanol and/or methane. Methane oxidation requires the enzyme methane monooxygenase (MMO)[2][3]. Methylotrophs with this enzyme are given the name methanotrophs. The oxidation of methane (or methanol) can be assimilatory or dissimilatory in nature (See Figure 1). If dissimilatory, the formaldehyde product will be oxidized completely into to produce reductant and energy[4][5]. If assimilatory, formaldehyde is used to synthesize a 3-Carbon () compound used for the production of biomass[1][6]. Many methylotrophs may use multi-carbon compounds for anabolism, limiting their use of formaldehyde to dissimilatory processes, while methanotrophs are generally limited to only metabolism.

Compounds known to support methylotrophic metabolism[6][7][8][9][10]
Single Carbon Compounds Chemical Formula Multi-Carbon Compounds Chemical Formula
Carbon monoxide Dimethyl ether
Formaldehyde Dimethylamine
Formamide Dimethyl sulfide
Formic acid Tetramethylammonium
Methane Trimethylamine
Methanol Trimethylamine N-oxide
Methylamine Trimethylsuphonium
Methyl halide
File:Common methylotrophic metabolic pathways.jpg
General steps of methylotrophic metabolism displaying 4 known assimilatory methylotrophic pathways. The general catabolic pathway is also shown. Q denotes a membrane-bound quinone.

Catabolism

Methylotrophs use the electron transport chain to transduce the energy from oxidation into . First, methane is oxidized to methanol by MMO, requiring 2 equivalents of reducing power and 1 molecule of dioxygen[3][4]. Organisms which have MMO are called methanotrophs. Methanol is then oxidized to formaldehyde through the action of either methanol dehydrogenase (MDH) in bacteria[11] or a non-specific alcohol oxidase in yeast[12]. Depending on the methylotroph, electrons from methanol oxidation are passed to cytochrome b or cytochrome c of the electron transport chain to produce for assimilatory processes[13].

In dissimilatory processes, formaldehyde is completely oxidized to and released. First, formaldehyde is oxidized to formate which directly provide electrons to cytochrome b or c of the electron transport chain[1][4]. In the case of associated dehydrogenases, is produced as well[6]. Formate is oxidized to which produces and for biosynthesis[14]. 

Anabolism

The main metabolic challenge for methylotrophs is the assimilation of single carbon units into biomass. Methylotrophs must form de novo carbon-carbon bonds with each 1-Carbon () molecule. There are four distinct assimilation pathways[1]. Bacteria use three of these pathways[6][10] while Fungi use only one[15]. The common theme of all four pathways is the usage of multi-carbon intermediates to incorporate 3 molecules, followed by a cleavage step which creates one new molecule for biomass. The other intermediates are rearranged to regenerate the original multi-carbon intermediates. 

Bacteria 

Each species of methylotrophic bacteria has a single dominant assimilation pathway[4]. The three characterized pathways for carbon assimilation are the ribulose monophosphate (RuMP) and serine pathways of formaldehyde assimilation as well as the ribulose bisphosphate (RuBP) pathway of CO2 assimilation[1][6][10][16]. 

Ribulose bisphosphate (RuBP) cycle

Unlike the other assimilatory pathways, bacteria using the RuBP pathway derive all of their organic carbon from assimilation[4][17].  This pathway was first elucidated in photosynthetic autotrophs and is better known as the Calvin Cycle[17][18]. Shortly thereafter, methylotrophic bacteria who could grow on reduced compounds were found using this pathway[19].

First, 3 molecules of ribulose 5-phosphate are phosphorylated to ribulose 1,5-bisphosphate (RuBP). The enzyme ribulose bisphosphate carboxylase (RuBisCO) carboxylates these RuBP molecules which produces 6 molecules of 3-phosphoglycerate (PGA). The enzyme phosphoglycerate kinase phosphorylates PGA into 1,3-diphosphoglycerate (DPGA). Reduction of 6 DPGA by the enzyme glyceraldehyde phosphate dehydrogenase generates 6 molecules of the compound glyceraldehyde-3-phosphate (GAP). One GAP molecule is diverted towards biomass while the other 5 molecules regenerate the 3 molecules of ribulose 5-phosphate[6][18].

Ribulose monophosphate (RuMP) cycle

A new pathway was suspected when RuBisCO was not found in the methanotroph Methylmonas methanica[20]. Through radio-labelling experiments, it was shown that M. methanica used the Ribulose monophate (RuMP) pathway. This has led researchers to propose that the RuMP cycle may have preceded the RuBP cycle[4]. 

Like the RuBP cycle, this cycle begins with 3 molecules of ribulose-5-phosphate. However, instead of phosphorylating ribulose-5-phosphate, 3 molecules of formaldehyde form a C-C bond through an aldol condensation, producing 3 molecules of 3-hexulose 6-phosphate (hexulose phosphate). One of these molecules of hexulose phosphate is converted into GAP and either pyruvate or dihydroxyacetone phosphate (DHAP). The pyruvate or DHAP is used towards biomass while the other 2 hexulose phosphate molecules and the molecule of GAP are used to regenerate the 3 molecules of ribulose-5-phosphate[5][20].

Serine cycle

Unlike the other assimilatory pathways, the serine cycle uses carboxylic acids and amino acids as intermediates instead of carbohydrates[4][21]. First, 2 molecules of formaldehyde are added to 2 molecules of the amino acid glycine. This produces two molecules of the amino acid serine, the key intermediate of this pathway.  These serine molecules eventually produce 2 molecules of 2-phosphoglycerate, with one molecule going towards biomass and the other being used to regenerate glycine. Notably, the regeneration of glycine requires a molecule of as well, therefore the Serine pathway also differs from the other 3 pathways by its requirement of both formaldehyde as well as [20][21]. 

Yeasts

Methylotrophic yeast metabolism differs from bacteria primarily on the basis of the enzymes used and the carbon assimilation pathway. Unlike bacteria which use bacterial MDH, methylotrophic yeasts oxidize methanol in their peroxisomes with a non-specific alcohol oxidase. This produces formaldehyde as well as hydrogen peroxide[22][23]. Compartmentalization of this reaction in peroxisomes likely sequesters the hydrogen peroxide produced. Catalase is produced in the peroxisomes to deal with this harmful by-product[15][22].

Dihydroxyacteone (DHA) cycle 

The dihydroxyacetone (DHA) pathway, also known as the xylulose monophosphate (XuMP) pathway, is found exclusively in yeast[22][24]. This pathway assimilates three molecules of formaldehyde into 1 molecule of DHAP using 3 molecules of xylulose 5-phosphate as the key intermediate.

DHA synthase acts as a transferase (transketolase) to transfer part of xylulose 5-phosphate to DHA. Then these 3 molecules of DHA are phosphorylated to DHAP by triokinase. Like the other cycles, 3 molecules are produced with 1 molecule being directed for use as cell material. The other 2 molecules are used to regenerate xylulose 5-phosphate[25].      CodeSwitch (talk) 05:28, 8 October 2017 (UTC) CodeSwitch (talk) 01:57, 9 October 2017 (UTC)

CodeSwitch (talk) 14:55, 2 November 2017 (UTC)

  1. ^ a b c d e Yurimoto, Hiroya; Kato, Nobuo; Sakai, Yasuyoshi (2005-01-01). "Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism". The Chemical Record. 5 (6): 367–375. doi:10.1002/tcr.20056. ISSN 1528-0691.
  2. ^ Nguyen, Ngoc-Loi; Yu, Woon-Jong; Yang, Hye-Young; Kim, Jong-Geol; Jung, Man-Young; Park, Soo-Je; Roh, Seong-Woon; Rhee, Sung-Keun (28 September 2017). "A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase". Journal of Microbiology. 55 (10): 775–782. doi:10.1007/s12275-017-7317-3.
  3. ^ a b Ross, Matthew O.; Rosenzweig, Amy C. (2017-04-01). "A tale of two methane monooxygenases". JBIC Journal of Biological Inorganic Chemistry. 22 (2–3): 307–319. doi:10.1007/s00775-016-1419-y. ISSN 0949-8257.
  4. ^ a b c d e f g Hanson, R. S.; Hanson, T. E. (1996-06-01). "Methanotrophic bacteria". Microbiological Reviews. 60 (2): 439–471. ISSN 1092-2172. PMID 8801441.
  5. ^ a b Vorholt, Julia A. (2002-10-01). "Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria". Archives of Microbiology. 178 (4): 239–249. doi:10.1007/s00203-002-0450-2. ISSN 0302-8933.
  6. ^ a b c d e f J Colby; H Dalton; Whittenbury, and R. (1979). "Biological and Biochemical Aspects of Microbial Growth on C1 Compounds". Annual Review of Microbiology. 33 (1): 481–517. doi:10.1146/annurev.mi.33.100179.002405. PMID 386931.
  7. ^ Oremland, Ronald S.; Kiene, Ronald P.; Mathrani, Indra; Whiticar, Michael J.; Boone, David R. (1989-04-01). "Description of an Estuarine Methylotrophic Methanogen Which Grows on Dimethyl Sulfide". Applied and Environmental Microbiology. 55 (4): 994–1002. ISSN 0099-2240. PMID 16347900.
  8. ^ Holmes, Andrew J.; Kelly, D. P.; Baker, Simon C.; Thompson, A. S.; Marco, Paolo De; Kenna, Elizabeth M.; Murrell, J. Colin (1997-01-01). "Methylosulfonomonas methylovora gen. nov., sp. nov., and Marinosulfonomonas methylotropha gen. nov., sp. nov.: novel methylotrophs able to grow on methanesulfonic acid". Archives of Microbiology. 167 (1): 46–53. doi:10.1007/s002030050415. ISSN 0302-8933.
  9. ^ Kelly, Don P.; Baker, Simon C.; Trickett, Jim; Davey, Margaret; Murrell, J. Colin (1994). "Methanesulphonate utilization by a novel methylotrophic bacterium involves an unusual monooxygenase". Microbiology. 140 (6): 1419–1426. doi:10.1099/00221287-140-6-1419.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  10. ^ a b c Firsova, Julia; Doronina, Nina; Lang, Elke; Spröer, Cathrin; Vuilleumier, Stéphane; Trotsenko, Yuri. "Ancylobacter dichloromethanicus sp. nov. – a new aerobic facultatively methylotrophic bacterium utilizing dichloromethane". Systematic and Applied Microbiology. 32 (4): 227–232. doi:10.1016/j.syapm.2009.02.002.
  11. ^ Duine, J.a.; Frank, J.; Berkhout, M.p.j. (1984-03-26). "NAD-dependent, PQQ-containing methanol dehydrogenase: a bacterial dehydrogenase in a multienzyme complex". FEBS Letters. 168 (2): 217–221. doi:10.1016/0014-5793(84)80249-5. ISSN 1873-3468.
  12. ^ Murray, William D.; Duff, Sheldon J. B.; Lanthier, Patricia H. (1989-11-01). "Induction and stability of alcohol oxidase in the methylotrophic yeast Pichia pastoris". Applied Microbiology and Biotechnology. 32 (1): 95–100. doi:10.1007/BF00164829. ISSN 0175-7598.
  13. ^ Verseveld, H. W. Van; Stouthamer, A. H. (1978-07-01). "Electron-transport chain and coupled oxidative phosphorylation in methanol-grown Paracoccus denitrificans". Archives of Microbiology. 118 (1): 13–20. doi:10.1007/BF00406068. ISSN 0302-8933.
  14. ^ Chistoserdova, Ludmila; Crowther, Gregory J.; Vorholt, Julia A.; Skovran, Elizabeth; Portais, Jean-Charles; Lidstrom, Mary E. (2007-12-15). "Identification of a Fourth Formate Dehydrogenase in Methylobacterium extorquens AM1 and Confirmation of the Essential Role of Formate Oxidation in Methylotrophy". Journal of Bacteriology. 189 (24): 9076–9081. doi:10.1128/jb.01229-07. ISSN 0021-9193. PMID 17921299.
  15. ^ a b van der Klei, Ida J.; Yurimoto, Hiroya; Sakai, Yasuyoshi; Veenhuis, Marten. "The significance of peroxisomes in methanol metabolism in methylotrophic yeast". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1763 (12): 1453–1462. doi:10.1016/j.bbamcr.2006.07.016.
  16. ^ TAYLOR, STEPHEN C.; DALTON, HOWARD; DOW, CRAWFORD S. (1981). "Ribulose-1,5-bisphosphate Carboxylase/Oxygenase and Carbon Assimilation in Methylococcus capsulatus (Bath)". Microbiology. 122 (1): 89–94. doi:10.1099/00221287-122-1-89.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  17. ^ a b Raines, Christine A. (2003-01-01). "The Calvin cycle revisited". Photosynthesis Research. 75 (1): 1–10. doi:10.1023/A:1022421515027. ISSN 0166-8595.
  18. ^ a b Champigny, Marie-Louise; Bismuth, Evelyne (1976-01-01). "Role of Photosynthetic Electron Transfer in Light Activation of Calvin Cycle Enzymes". Physiologia Plantarum. 36 (1): 95–100. doi:10.1111/j.1399-3054.1976.tb05034.x. ISSN 1399-3054.
  19. ^ Taylor, Stephen; Dalton, Howard; Dow, Crawford (1980-07-01). "Purification and initial characterisation of ribulose 1,5-bisphosphate carboxylase from Methylococcus capsulatus (Bath)". FEMS Microbiology Letters. 8 (3): 157–160.
  20. ^ a b c Quayle, J. R. (1980-02-01). "Microbial assimilation of C1 compounds". Biochemical Society Transactions. 8 (1): 1–10. doi:10.1042/bst0080001. ISSN 0300-5127. PMID 6768606.
  21. ^ a b Chistoserdova, L. V.; Lidstrom, M. E. (1994-12-01). "Genetics of the serine cycle in Methylobacterium extorquens AM1: identification, sequence, and mutation of three new genes involved in C1 assimilation, orf4, mtkA, and mtkB". Journal of Bacteriology. 176 (23): 7398–7404. doi:10.1128/jb.176.23.7398-7404.1994. ISSN 0021-9193. PMID 7961516.
  22. ^ a b c Yurimoto, Hiroya; Oku, Masahide; Sakai, Yasuyoshi (2011). "Yeast Methylotrophy: Metabolism, Gene Regulation and Peroxisome Homeostasis". International Journal of Microbiology. 2011: 1–8. doi:10.1155/2011/101298. ISSN 1687-918X.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  23. ^ Gonchar, Mykhailo; Maidan, Mykola; Korpan, Yaroslav; Sibirny, Volodymyr; Kotylak, Zbigniew; Sibirny, Andrei (2002-08-01). "Metabolically engineered methylotrophic yeast cells and enzymes as sensor biorecognition elements". FEMS Yeast Research. 2 (3): 307–314. doi:10.1016/s1567-1356(02)00124-1. ISSN 1567-1356.
  24. ^ Gleeson, M. A.; Sudbery, P. E. (1988-03-01). "The methylotrophic yeasts". Yeast. 4 (1): 1–15. doi:10.1002/yea.320040102. ISSN 1097-0061.
  25. ^ WAITES, M. J.; QUAYLE, J. R. (1981). "The Interrelation between Transketolase and Dihydroxyacetone Synthase Activities in the Methylotrophic Yeast Candida boidinii". Microbiology. 124 (2): 309–316. doi:10.1099/00221287-124-2-309.{{cite journal}}: CS1 maint: unflagged free DOI (link)
Retrieved from "https://en.wikipedia.org/w/index.php?title=User:CodeSwitch/sandbox&oldid=810247293"