User talk:CodeSwitch/sandbox

Bacterial Circadian Rhythms
This article needs a section after the lead that better explains what circadian rhythms are and their general role in organisms. A section discussing why bacterial circadian rhythms need to synchronize with the environment should be created and updated with current understanding. The section “Relationship to Cell Division” should discuss how bacterial circadian rhythms gate-keep for cell division. The section “Global regulation… chromosome topology” should explain the choice of using cyanobacteria for elucidating circadian rhythms instead of eukaryotes and elaborate on chromosomal compaction due to circadian rhythms. The “molecular mechanism” section regarding KaiABC proteins needs updating as it doesn’t discuss the reciprocal interplay between the Kai proteins   and doesn’t explain the post-translational regulation mechanism adequately.

Other significant proteins in bacterial circadian rhythms such as SasA, CikA  and RpaA  should also be discussed. New research such as the successful transplantation of KaiABC proteins in prokaryotes other than cyanobacteria and how diurnal variation of gut bacteria influence mouse circadian rhythms should be added.

Some general improvements might include simplifying diction and shortening section headings. The section “Adaptive Significance” shouldn’t begin with a question and the extrapolation to “all organisms” is suspect and should be cited or removed, along with phrases such as “seemed reasonable”, exquisitely precise”, “while intuitive”, “persuasive evidence… is lacking”, and “Cyanobacteria are… of the few organisms…”. All references are from peer-reviewed journals with no obvious bias towards any single source, however, proper hyperlinks need to be added. CodeSwitch (talk) 19:09, 16 September 2017 (UTC) CodeSwitch (talk) 19:06, 16 September 2017 (UTC) CodeSwitch (talk) 20:18, 17 September 2017 (UTC)

Reflection
I learned during my evaluation of this article that it is difficult to write a quality Wikipedia entry. Finding current/updated research for my critique was very easy, likely because there has been little activity on this page. The word count was difficult so I primarily focused on content. In the future, it may be beneficial to assign 250 characters for content improvement (new/updated research) and 250 characters for some of the probing questions. CodeSwitch (talk) 02:39, 18 September 2017 (UTC)

Assignment 2 - Methylotroph
Methylotrophs are a notable subject because they have a unique metabolism that has been well documented since 1892. Methylotrophs have been found in wetlands, oceans , soil   , plants  , deserts , lake sediment   , soda lakes  , volcanic mud pots , the human body  and even Antarctica  , highlighting their global significance. Based on keyword search in literature databases, there are over 500 publications on methylotrophs and almost 800 publications based on methanotrophs (a subset of methylotrophs), exemplifying the importance of this unique metabolic ability in ecological     , commercial       and bio-remedial  activities.

Despite the available information, the current Methylotroph page contains scant information which is often misconstrued and uncited. My focus will be on the “General Microbiology” section because it is almost entirely composed of contradictory, false or irrelevant statements, potentially due to relying heavily on one source. The manifests in the careless suggestion that methylotrophy is limited to bacteria, omitting methylotrophic yeasts  and Archaea. Then a faulty generalization is made regarding cellular structure, simultaneously suggesting that methanotrophs are not methylotrophs despite the two not being mutually exclusive. This leads to another incorrect statement suggesting that there is “a single obligate methylotroph” despite overwhelming evidence of many obligate C1 organisms      , many of which are methanotrophs    (and hence also methylotrophs).

The rest of this section continues with generalizations on structure that do not apply to a significant amount of methylotrophs. By focusing on structure, which varies between methylotrophs, the article fails to discuss the one thing all methylotrophs share- the ability to shunt single carbon units into metabolic pathways. Further subdivisions such as Obligate/Facultative, Methanotrophic/Non-Methanotrophic and Bacteria/Archaea/Fungi can, and should be made in subsequent edits, because there are certainly within-group structural similarities.

However, my focus will be on the general theme of producing and oxidizing formaldehyde, a central intermediate used in the assimilatory and dissimilatory processes of all methylotrophs. A common dissimilatory pathway  and the main assimilatory pathways (RuBP, RuMP , Serine  , and XuMP   ) that use formaldehyde will be discussed in detail along with important intermediates and products. However, enzymes and structures used for these pathways differ and only the most common will be addressed for the reader’s sake.

Note: I realize I forgot to sign off with 4 tildes originally. Please refer to edit history to see timestamp indicating I handed in this assignment on time. Thank you. CodeSwitch (talk) 05:19, 7 October 2017 (UTC)

CodeSwitch's Peer Review
Critique Addition of the section is highly warranted and significantly improves the quality of the article as metabolism is a fundamental aspect of Methylotrophy. Coverage is neutral and balanced as numerous credible sources are presented from a wide range of topics in Methylotrophy.

The figure is very well done, though I suggest altering the placement of the figure so that it’s more closely associated with the anabolism section, where it's more relevant. This will better complement its purpose as a visual aid. I also suggest explaining the significance of the difference between single-carbon and multi-carbon compounds to justify the relevance of the information in the table. For example, the use of 1-Carbon compounds by certain methanogens allows them to avoid competition for these substrates. Other methylotrophs are able to derive all of their carbon and energy from a single multi-carbon compound. This type of information, as supported by the literature, would make the purpose of the table much clearer to readers.

The talk page mentions that the diversity of Methylotrophic metabolism should be better represented, especially by including a discussion on Yeast. While I agree that this is important information to include to ensure broad coverage, the section on yeast seems out of place, as the majority of the section is dedicated to discussing different pathways. Discussion of the DHA cycle is well done and should be included under "Metabolism" though it’s possible that the explanation on methylotrophic yeasts deserves its own subsection, for organizational purposes and to allow for further expansion on this topic.

The information for each pathway is well presented and consistent; some background information is first given and the mechanisms behind each pathway follows, guiding the reader’s understanding. One suggestion is that the different pathways be presented in the order in which they are introduced, to improve the organization and flow of information.

Minor Edits (not to be marked)

The key intermediate behind methylotrophic metabolism is formaldehyde which can be diverted to either catabolism or anabolism. Methylotrophs arrive at formaldehyde through oxidation of methane or methanol. Methane oxidation 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 CO2 to produce reductant and energy. If assimilatory, formaldehyde is used to synthesize a 3-Carbon (C3) compound used for the production of biomass

Catabolism Methylotrophs use the electron transport chain to transduce the energy from oxidation into 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 either methanol dehydrogenase (MDH) in bacteria or a non-specific alcohol oxidase in yeast. Depending on the methylotroph, electrons from methanol oxidation are passed to cytochrome b or cytochrome c of the electron transport chain to produce ATP for assimilatory processes. In dissimilatory processes, formaldehyde is completely oxidized to CO2 and released. First, formaldehyde is oxidized to formate which directly provide electrons to cytochrome b or c of the electron transport chain. In the case of NAD+ associated dehydrogenases, NADH is produced as well. Formate is oxidized to CO2 which produces NADH and ATP for biosynthesis.

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 (C1) molecule (Through de novo synthesis, Methylotrophs must for carbon-carbon bonds with each 1-Carbon (C1) molecule). There are four distinct assimilation pathways. Bacteria use three of these pathways while Fungi use only one. The common theme of all four pathways is the usage of multi-carbon intermediates to incorporate 3 C1 molecules, followed by a cleavage step which creates one new C3 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. 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 the other assimilatory pathways, bacteria using the RuBP pathway derive all of their organic carbon from CO2 assimilation. This pathway was first elucidated in photosynthetic autotrophs and is better known as the Calvin Cycle. Shortly thereafter, methylotrophic bacteria who could grow on reduced C1 compounds were found using this pathway.

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 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 new pathway was suspected when RuBisCO was not found in the methanotroph Methylmonas methanica. 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.

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 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 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 of 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 (change as well as to and).

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. 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.

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 C3molecules are produced with 1 molecule being directed for use as cell material. The other 2 molecules are used to regenerate xylulose 5-phosphate.

MackenzieGutierrez (talk) 04:01, 8 November 2017 (UTC)