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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. Methane monooxygenase (MMO) and Formate dehydrogenase (FDH) may be membrane-associated or cytoplasmic while Methanol dehydrogenase (MDH) and Formaldehyde dehydrogenase (FALDH) are always membrane-associated.

Catabolism

Methylotrophs use the electron transport chain to conserve the energy from the oxidation steps. For methanotrophs, an activation step is required to make chemically-stable methane amenable for further degradation. This oxidation to methanol is catalyzed by MMO which incorporates 1 oxygen atom into methane and reduces the other oxygen atom to water, which requires 2 equivalents of reducing power[3][4]. 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]. Electrons from methanol oxidation are passed to a membrane-associated quinone of the electron transport chain to produce [13].

In dissimilatory processes, formaldehyde is completely oxidized to and released. Formaldehyde is oxidized to formate via the action of Formaldehyde dehydrogenase (FALDH) which directly provide electrons to a membrane associated quinone of the electron transport chain, usually cytochrome b or c[1][4]. In the case of associated dehydrogenases, is produced[6]. Formate is oxidized to by cytoplasmic or membrane-bound Formate dehydrogenase (FDH) which produces [14]. 

Anabolism

The main metabolic challenge for methylotrophs is the assimilation of single carbon units into biomass. Through de novo synthesis, Methylotrophs must form carbon-carbon bonds with each 1-Carbon () molecule. This is an energy intensive process which facultative methylotrophs avoid by using a range of larger organic compounds[15]. However, obligate methylotrophs must assimilate molecules. There are four distinct assimilation pathways with the common theme of generating one molecule [1]. Bacteria use three of these pathways[6][10] while Fungi use one[16]. All four pathways use multi-carbon intermediates to incorporate the 3 molecules into, then perform a cleavage step which creates a new molecule for biomass. The remaining 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][17]. 

Ribulose bisphosphate (RuBP) cycle

Unlike the other assimilatory pathways, bacteria using the RuBP pathway derive all of their organic carbon from assimilation[4][18].  This pathway was first elucidated in photosynthetic autotrophs and is better known as the Calvin Cycle[18][19]. Shortly thereafter, methylotrophic bacteria who could grow on reduced compounds were found using this pathway[20].

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][19].

Ribulose monophosphate (RuMP) cycle

A new pathway was suspected when RuBisCO was not found in the methanotroph Methylmonas methanica[21]. 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][21].

Serine cycle

Unlike the other assimilatory pathways, the serine cycle uses carboxylic acids and amino acids as intermediates instead of carbohydrates[4][22]. 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 [21][22]. 

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[23][24]. 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[16][23].

Dihydroxyacteone (DHA) cycle 

The dihydroxyacetone (DHA) pathway, also known as the xylulose monophosphate (XuMP) pathway, is found exclusively in yeast[23][25]. 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[26].      CodeSwitch (talk) 05:28, 8 October 2017 (UTC) CodeSwitch (talk) 01:57, 9 October 2017 (UTC)

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

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