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Original "General microbiology" (Article = Methylotroph)

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 "Metabolism" (Article = Methylotroph)

The key intermediate behind methylotrophic metabolism is formaldehyde as it can be diverted to either catabolism or anabolism. Organisms typically arrive at formaldehyde through oxidation of methane or methanol. Not all methylotrophs can oxidize methane as this requires the enzyme methane monooxygenase (MMO). 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 ${\ce {CO2}}$ to produce reductant and energy. If assimilatory, formaldehyde is used to synthesize a 3-Carbon (${\ce {C3}}$) compound used for the production of biomass.

Compounds known to support methylotrophic metabolism

Single Carbon Compounds	Chemical Formula	Multi-Carbon Compounds	Chemical Formula
Carbon monoxide	${\ce {CO}}$	Dimethyl ether	${\ce {(CH3)2O}}$
Formaldehyde	${\ce {CH2O}}$	Dimethylamine	${\ce {(CH3)2NH}}$
Formamide	${\ce {HCONH2}}$	Dimethyl sulfide	${\ce {(CH3)2S}}$
Formic acid	${\ce {HCOOH}}$	Tetramethylammonium	${\ce {(CH3)4N+}}$
Methane	${\ce {CH4}}$	Trimethylamine	${\ce {(CH3)3N}}$
Methanol	${\ce {CH3OH}}$	Trimethylamine N-oxide	${\ce {(CH3)3NO}}$
Methylamine	${\ce {CH3NH2}}$	Trimethylsuphonium	${\ce {(CH3)3S+}}$
Methyl halide	${\ce {CH3X}}$

Catabolism

Methylotrophs use the electron transport chain to transduce energy from oxidation into ${\ce {ATP}}$. First, methane is oxidized to methanol by MMO, requiring 2 equivalents of reducing power and 1 molecule of dioxygen. Organisms which have MMO are called methanotrophs. Methanol is then oxidized to formaldehyde through the action of methanol dehydrogenase (MDH) in bacteria or a non-specific alcohol oxidase in yeast. Electrons from methanol oxidation are passed to cytochrome c of the electron transport chain to produce ${\ce {ATP}}$ for assimilatory processes.

In dissimilatory processes, formaldehyde is completely oxidized to ${\ce {CO2}}$. First, formaldehyde is oxidized to formate. The dehydrogenase used for this process varies between methylotrophs with examples such as formaldehyde dehydrogenase or non-specific aldehyde dehydrogenases. Formaldehyde oxidation can directly provide electrons to cytochrome b or c of the electron transport chain for the production of ${\ce {ATP}}$. In the case of ${\ce {NAD+}}$ associated dehydrogenases, it can produce reducing power in the form of ${\ce {NADH}}$. Finally, formate is oxidized to ${\ce {CO2}}$ through either an ${\ce {NAD+}}$ associated or membrane bound formate dehydrogenase. The membrane bound dehydrogenase is responsible for donating electrons to cytochrome b while the ${\ce {NAD+}}$ associated dehydrogenase produces ${\ce {NADH}}$ for ${\ce {ATP}}$ production or biosynthesis. 

Anabolism

The main metabolic challenge for methylotrophs is the assimilation of single carbon units into biomass. In heterotrophs, the substrate usually has carbon-carbon bonds already (e.g. Glucose). However, methylotrophs must form new carbon-carbon bonds between their 1-Carbon (${\ce {C1}}$) molecules. This is accomplished in different ways depending on which of the four assimilation cycles is used. Bacteria use three of these pathways while Archaea use only one. The common theme of all four pathways is the usage of multi-carbon intermediates to join incorporate 3 ${\ce {C1}}$ molecules, followed by a cleavage step which creates one new ${\ce {C3}}$ molecule for building 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. 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. 

Ribulose bisphosphate (RuBP) cycle

Unlike organisms using the other assimilatory pathways, bacteria using the RuBP pathway derive all of their biomass from the assimilation of ${\ce {CO2}}$.  This pathway was first elucidated in photosynthetic autotrophs and is better known as the Calvin Cycle. Shortly after this discovery, methylotrophic bacteria who could grow on reduced ${\ce {C1}}$ compounds were found using the RuBP pathway.

First, 3 molecules of ribulose 5-phosphate are phosphorylated to ribulose 1,5-bisphosphate (RuBP). Then the enzyme ribulose bisphosphate carboxylase (RuBisCO) carboxylates these three RuBP molecules which generates 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 ${\ce {C3}}$ 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.

Ribulose monophosphate (RuMP) cycle

A cycle different than the RuBP pathway was suspected when researchers did not find the enzyme RuBisCO in the bacteria Methylmonas methanica while it was growing on methane. Through radio-labelled carbon experiments, it was shown that the cycle M. methanica used was indeed different from the RuBP pathway and has even led researchers to propose that the RuMP cycle may have preceded the RuBP cycle. 

Like the RuBP cycle, this cycle begins with 3 molecules of ribulose-5-phosphate. However, instead of phosphorylation, 3 molecules of formaldehyde form a C-C bond through an aldol condensation reaction, producing 3 ${\ce {C6}}$ 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.

Serine cycle

Unlike the other 3 assimilatory pathways, the serine cycle uses carboxylic acids and amino acids as intermediates instead of carbohydrates. 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 in this pathway.  These serine molecules eventually produce 2 molecules of 2-phosphoglycerate, with one C3 molecule going towards biomass and the other being used to regenerate glycine. Notably, the regeneration of glycine requires a molecule of CO2 as well, therefore the Serine pathway also differs from the other 3 pathways by its requirement of both formaldehyde as well as CO2. 

Yeasts

Yeasts differ from bacteria in their metabolism primarily on the basis of the enzymes they use and their carbon assimilation pathway. Unlike bacteria which use bacterial MDH, methylotrophic yeasts perform methanol oxidation in their peroxisomes with a non-specific alcohol oxidase which produces formaldehyde as well as hydrogen peroxide. Yeast compartmentalize this reaction in peroxisomes likely to sequester the hydrogen peroxide produced. Catalase is produced in the peroxisomes to deal with this harmful by-product.

Dihydroxyacteone (DHA) cycle 

The dihydroxyacetone (DHA) pathway, also known as the xylulose monophosphate (XuMP) pathway, is found exclusively in yeast. 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 C3 molecules are produced with 1 molecule being directed for use as cell material. The other 2 molecules are used to regenerate xylulose 5-phosphate.      CodeSwitch (talk) 05:28, 8 October 2017 (UTC)