User talk:Osolodova/sandbox

"Lignin-modifying enzymes"

Lignin-modifying enzymes (LMEs) are various types of enzymes produced by fungi and bacteria that catalyze the breakdown of lignin, a biopolymer commonly found in the cell walls of plants. The terms ligninases and lignases are older names for the same class, but the name "lignin-modifying enzymes" is now preferred, given that these enzymes are not hydrolytic but rather oxidative (electron withdrawing) by their enzymatic mechanisms. LMEs include peroxidases, such as lignin peroxidase (EC 1.11.1.14), manganese peroxidase (EC 1.11.1.13), versatile peroxidase (EC 1.11.1.16), and many phenoloxidases of the laccase type.

LMEs have been known to be produced by many species of white rot basidiomycetous fungi, including: Phanerochaete chrysosporium, Ceriporiopsis subvermispora, Trametes versicolor, Phlebia radiata, Pleurotus ostreatus and Pleurotus eryngii.

LMEs are produced not only by white rot fungi but also by litter-decomposing basidiomycetous fungi such as Agaricus bisporus (common button mushroom), and many Coprinus and Agrocybe species. The brown rot fungi, which are able to colonize wood by degrading cellulose, are only able to partially degrade lignin.

Some bacteria also produce LMEs, although fungal LMEs are more efficient in lignin degradation. Fungi are thought to be the most substantial contributors to lignin degradation in natural systems.

LMEs and cellulases are crucial to ecologic cycles (for example, growth/death/decay/regrowth, the carbon cycle, and soil health) because they allow plant tissue to be decomposed quickly, releasing the matter therein for reuse by new generations of life.

Bacterial lignin-modifying enzymes

Although much research has been done to understand fungal LMEs, only recently has more focus been placed on characterizing these enzymes in bacteria. The main LMEs in both fungi and bacteria are peroxidases and laccases.

Although bacteria lack homologs to the most common fungal peroxidases (lignin peroxidase, manganese peroxidase, and versatile peroxidase), many produce dye decolourizing peroxidases (DyP-type peroxidases). Bacteria from a variety of classes express DyP peroxidases, including Gammaproteobacteria, Firmicutes, and Actinobacteria. Peroxidases depolymerize lignin by oxidation using hydrogen peroxide. Fungal peroxidases have higher oxidizing power than bacterial DyP-type peroxidases studied so far, and are able to degrade more complex lignin structures. DyP-type peroxidases have been found to work on a large range of substrates, including synthetic dyes, monophenolic compounds, lignin-derived compounds, and alcohols.

Laccases, which are multicopper oxidases, are another class of enzymes found in both bacteria and fungi which have significant lignin-degrading properties. Laccases degrade lignin by oxidation using oxygen. Laccases are also widely distributed among bacterial species, including Bacillus subtilis, Caulobacter crescentus, Escherichia coli and Mycobacterium tuberculosum. Like DyP-type peroxidases, bacterial laccases have a wide substrate range.

There is interest in using bacterial laccases and DyP peroxidases for industry applications, biotechnology and bioremediation because of the greater ease of manipulation of bacterial genomes and gene expression compared to fungi. The wide range of substrates for these types of enzymes also increases the range of processes they may be used in. These processes include pulp processing, textile dye modification, decontamination of waste water and production of pharmaceutical building blocks. Furthermore, bacterial laccases function at higher temperatures, alkalinity, and salt concentrations than fungal laccases, making them more suitable for industrial use.

Both intracellular and extracellular bacterial DyP-type peroxidases and laccases have been identified, suggesting that some are used as intracellular enzymes while others are secreted to degrade compounds in the environment. However, their roles in bacterial physiology and their natural physiological substrates have yet to be detailed.

Osolodova (talk) 01:11, 20 November 2017 (UTC)

Assignment 3: Article Edit

Original: "Lignin-modifying enzyme"

Lignin-modifying enzymes (LMEs) are various types of enzymes produced by fungi that catalyze the breakdown of lignin, a biopolymer commonly found in the cell walls of plants. The terms ligninases and lignases are older names for the same class, but the name "lignin-modifying enzymes" is now preferred, given that these enzymes are not hydrolytic but rather oxidative (electron withdrawing) by their enzymatic mechanisms. LMEs include peroxidases, such as lignin peroxidase (EC 1.11.1.14), manganese peroxidase (EC 1.11.1.13), versatile peroxidase (EC 1.11.1.16), and many phenoloxidases of the laccase type.

LMEs have been known to be produced by many species of so-called white rot basidiomycetous fungi, including: Phanerochaete chrysosporium, Ceriporiopsis subvermispora, Trametes versicolor, Phlebia radiata, Pleurotus ostreatus and Pleurotus eryngii.

LMEs are produced not only by wood-white rotting fungi but also by litter-decomposing basidiomycetous fungi such as Agaricus bisporus (common button mushroom), and many Coprinus and Agrocybe species. The brown-rot fungi, which are able to colonize wood by degrading cellulose, are not able to produce LMEs.

Some results on LME-type of peroxidases have also been reported for some species of filamentous bacteria such as Streptomyces viridosporus T7A, Streptomyces lavendulae REN-7 and Clostridium stercorarium.

However, efficient lignin and lignin-like polymer degradation is only achieved by fungal LME peroxidases, and laccases in combinations with organic charge transfer mediator compounds. Laccases are more widely distributed enzymes belonging to the multicopper oxidase (MCO) superfamily encompassing all three domains of life (bacteria, archaea, eukarya).

LMEs and cellulases are crucial to ecologic cycles (for example, growth/death/decay/regrowth, the carbon cycle, and soil health) because they allow plant tissue to be decomposed quickly, releasing the matter therein for reuse by new generations of life.

Edits - "Lignin-modifying enzyme"

Bacterial Lignin-modifying Enzymes

Although much research has been done to understand fungal LMEs, only recently has more focus been placed on characterizing these enzymes in bacteria. Most LMEs are peroxidases, and although bacteria generally lack homologs to the most common fungal LMEs, they are rich in another type of peroxidase - dye decolourizing peroxidases (DyP-type peroxidases). The first enzyme belonging to this family was characterized in fungi in 1999 as a dye-degrading enzyme before bacterial counterparts were discovered. Bacteria from a variety of phyla express DyP peroxidases, including Gammaproteobacteria, Firmicutes, and Actinobacteria.

Both intracellular and extracellular bacterial DyP-type peroxidases have been identified, suggesting that some are used as intracellular enzymes while others are secreted to degrade compounds in the environment. DyP-type peroxidases have been found to work on a large range of substrates, including synthetic dyes, monophenolic compounds, lignin-derived compounds, and alcohols. However, their roles in bacterial physiology and their natural physiological substrates have yet to be detailed.

Although fungal counterparts of bacterial DyP-type peroxidases have more potency in terms of their lignin-degradation ability, bacterial DyP-type peroxidases have more potential for industry applications since manipulating genomes and gene expression in fungi is much more complicated than in bacteria.

Laccases, which are multicopper oxidases, are another class of enzymes found in both bacteria and fungi which have significant lignin-degrading properties. Like bacterial DyP-type peroxidases, bacterial laccases have yet to be fully understood and characterized. There is also interest in using these for industry applications, biotechnology and bioremediation because they have stronger degradation ability compared to DyP-type peroxidases and also have a wide substrate range. Again, laccases of bacterial origin show more potential for applications due to greater ease of manipulation.

Osolodova (talk) 21:42, 8 October 2017 (UTC)

'Lignin modifying enzyme' Wikipedia Article Critique (Assignment 2)

The topic of lignin modifying enzymes (LMEs) is a highly notable area of active research. There are numerous peer-reviewed research articles investigating modes of action of bacterial and fungal LMEs, newly discovered LME-producing organisms, and possible applications to bioremediation and industrial processes requiring lignin degradation. Since they are the only enzymes capable of lignin polymer degradation, LMEs are integral to plant biomass cycling through ecosystems and many studies have been done to better understand them. Furthermore, LMEs have a variety potential applications. Their use in breakdown of agricultural herbicides, biopulping processes, processing of feedstocks containing lignin, production of aromatic components of pharmaceutical drugs, and textile dye decolourization are currently being explored. LMEs have potential to further optimize these processes, thereby increasing profitability and efficiency.

The Wikipedia article on the topic of LMEs lacks references and fails to cover key areas, particularly their applications and bacterial source. Furthermore, some of the article’s information is inaccurate. For example, its claim that few bacteria are capable of producing LMEs is false. The inaccuracy of information on bacterial LMEs, and absence of information on LME applications, likely reflects the recency of research in these areas. It was only in 2009 that the ability of bacterial LMEs to degrade lignin was characterized.

To improve this article, a section could be added detailing this information. To date, most research has been done on LMEs in fungi, but more focus is now being placed on understanding these enzymes in bacteria. Fungi produce several LME classes, primarily lignin peroxidases, manganese peroxidases, versatile peroxidases and laccases, while the most effective LMEs produced by bacteria are dye decolourizing peroxidases and laccases. It has also been discovered that LMEs are widespread among bacteria. In terms of LME applications, bacteria are better candidates for enzyme production at a large scale. This is because fungal genomes and gene expression are more difficult to manipulate, and fungal LMEs are more complicated in structure.

Osolodova (talk) 06:40, 28 September 2017 (UTC)

Osolodova (talk) 04:29, 28 September 2017 (UTC)

'Peptidoglycan' Wikipedia Article Critique (Assignment 1)

Two weaknesses of the Wikipedia article “Peptidoglycan” are plagiarism and inadequate references. Some parts are almost directly copied from their sources (the sentences leading up to the first reference, for example), while others are somewhat closely paraphrased (the first paragraph under ‘Biosynthesis’). Additionally, the first reference is a blog, an unreliable source. Often, uncited statements are made, such as the importance of peptidoglycan in attachment in Gram positive bacteria (in the introduction), the amino acids in the peptidoglycan of E. coli and S. aureus (under ‘Structure’), and lysozyme’s action on peptidoglycan (under ‘Inhibition’). The fifth reference link also doesn’t lead to a source. Furthermore, the longest section, ‘Biosynthesis’, is based on one source; it would be improved if multiple were used.

In addition to these issues, disorganization and both excess and insufficient detail in certain topics decrease the article’s coherence. The differences between peptidoglycan structure in Gram positive and negative bacteria (in the introduction) could be made into a separate section. The last paragraph and diagram under ‘Structure’ would fit better under ‘Biosynthesis’. Specific details of the peptidoglycan of E. coli and S. aureus are unnecessary (under ‘Structure’). The ‘Biosynthesis’ section could be more concise and simply explained, with a diagram included to increase clarity. More information could be added about mechanisms of peptidoglycan-targeting antibiotics (under ‘Inhibition’), as this is a prevalent mode of antibiotic action. Finally, a section could be included on peptidoglycan’s role in Gram staining, which is also suggested in the article’s ‘Talk’ section.

—Osolodova (talk) 19:53, 17 September 2017 (UTC)

Critique Reflection (Assignment 1)

This assignment made me much more aware of the lack of references and amount of plagiarism that even a relatively notable topic like 'Peptidoglycan' can have. I was surprised to learn the importance of checking references on Wikipedia. Furthermore, many of the citations in the article led to online research articles or textbooks which could not be accessed without purchase, which made it very difficult to check the accuracy/reliability of the information in the Wikipedia article.

—Osolodova (talk) 22:48, 17 September 2017 (UTC)

Osolodova's Peer Review

The edited content is an appropriate change because a new section with more information about bacterial LMEs was added. It also contains a clear description which can give the readers a good understanding of this notable topic. However, very similar information about the applications of the bacterial enzymes appears twice in different paragraphs. To make the content more organized, I would suggest summarizing the application potential of both enzymes into one paragraph.

In general, the newly added content is important and relevant to the topic since the original article really lacked information about bacterial enzymes in lignin degradation. It is also acceptable that the edited material does not describe much about the enzymes' roles in bacterial physiology due to limited discoveries in this research area. But the inaccurate information on bacterial LMEs in the original article has not been edited. It still gives a sense that few bacteria can generate LMEs. I would also suggest giving a background about lignin degradation such as enzymatic combustion and reactions related to peroxidases and laccases to make the article better.

The work is concisely written, a new section has been made with accurate and easily understood words. It is also neutral since no content is about convincing the readers and there is no bias from the editor's own opinions.

The statements are connected to reliable sources. It is also balanced since the statements are from different sources with various aspects such as types, origins, and applications about bacterial LMEs. A possible improvement would be to confirm the content of the original article with several sources because it is hard to tell which part of it is real and accurate.

Overall, this edited material is neutral and balanced with many reliable sources. Although, some general information can still be added to make it better. Miaoran Li (talk) 07:26, 9 November 2017 (UTC)