User:Awilson0/sandbox

Original – "Biodegradation"
Biodegradation of lignin by white rot fungi leads to destruction of wood on the forest floor and human-made structures such as fences and wooden buildings. However biodegradation of lignin is a necessary prerequisite for processing biofuel from plant raw materials. Current processing setups show some problematic residuals after processing the digestible or degradable contents. The improving of lignin degradation would drive the output from biofuel processing to better gain or better efficiency.

Lignin is indigestible by animals, which lack the enzymes that can degrade this complex polymer. Some fungi (such as the Dryad's saddle) and bacteria do however biodegrade lignin using so-called ligninases (also named lignases). The mechanism of the biodegradation is speculated to involve free radical pathways. Well understood ligninolytic enzymes are manganese peroxidase and lignin peroxidase. Because it is cross-linked with the other cell wall components and has a high molecular weight, lignin minimizes the accessibility of cellulose and hemicellulose to microbial enzymes such as cellobiose dehydrogenase. Hence, in general lignin is associated with reduced digestibility of the overall plant biomass, which helps defend against pathogens and pests. Syringyl (S) lignol is more susceptible to degradation by fungal decay as it has fewer aryl-aryl bonds and a lower redox potential than guaiacyl units. This means that organic matter that is enriched with G lignol (like the bark of woody vascular plants) is more resistant to microbial attack.

Lignin is degraded by micro-organisms including fungi and bacteria. Lignin peroxidase (also "ligninase", EC number 1.14.99) is a hemoprotein firstly isolated from the white-rot fungus Phanerochaete chrysosporium  with a variety of lignin-degrading reactions, all utilizing hydrogen peroxide as an oxygen source. Other microbial enzymes may be involved in lignin biodegradation, such as manganese peroxidase and the copper-based laccase.

Edited – "Biodegradation"
Lignin is a very recalcitrant biopolymer, meaning that only certain species have the enzymes that are required to degrade it. Since lignin is a heteropolymer which differs by species and plant tissue type, some lignin is more recalcitrant than others. For example, syringyl (S) lignol is more susceptible to degradation by fungal decay as it has fewer aryl-aryl bonds and a lower redox potential than guaiacyl units. Because it is cross-linked with the other cell wall components, lignin minimizes the accessibility of cellulose and hemicellulose to microbial enzymes, leading to a reduced digestibility of biomass.

The main classes of ligninolytic enzymes are heme peroxidases such as lignin peroxidases, manganese peroxidases, versatile peroxidases, and dye-decolourizing peroxidases as well as copper-based laccases. Lignin peroxidases are able to oxidize non-phenolic lignin, whereas manganese peroxidases are only able to oxidize the phenolic structures. Dye-decolorizing peroxidases, or DyPs, exhibit catalytic activity on a very wide range of lignin model compounds, but their in vivo substrate has not yet been discovered. In general, laccases oxidize phenolic substrates but some fungal laccases have been shown to oxidize non-phenolic substrates in the presence of synthetic redox mediators.

Lignin Degradation in Fungi
The best-studied ligninolytic enzymes are found in Phanerochaete chrysosporium  and other white rot fungi. Some white rot fungi, such as C. subvermispora, can preferentially degrade the lignin in lignocellulose but others lack this ability. Most fungal lignin degradation involves secreted peroxidases which break lignin down into smaller molecules. Many fungal laccases are also secreted to assist in the degradation of phenolic lignin-derived compounds, though several intracellular fungal laccases have also been described. An important aspect of fungal lignin degradation is the activity of accessory enzymes to produce the H2O2 required for the function of lignin peroxidase and other heme peroxidases.

Lignin Degradation in Bacteria
Bacteria lack most of the enzymes involved in fungal lignin degradation, so their ligninolytic activity has not been studied extensively even though it was first described in 1930. Recently, however, many bacterial DyPs have been characterized and the role of bacteria in lignin degradation is being researched more heavily. Bacteria do not express any of the plant-type peroxidases (lignin peroxidase, Mn peroxidase, or versatile peroxidases) but three of the four classes of DyP are only found in bacteria. In contrast to fungi, most bacterial enzymes involved in lignin degradation are intracellular, including two classes of DyP and most bacterial laccases. Bacterial laccases tend to be more thermostable than their fungal counterparts so they are potentially more useful in industrial processes.