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Fungal extracellular enzyme activity
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<h2 id="factors-influencing-extracellular-enzyme-activity">Factors influencing extracellular enzyme activity</h2> <p>Extracellular enzyme production supplements the direct uptake of nutrients by microorganisms and is linked to nutrient availability and environmental conditions. The varied chemical structure of <a href="/facts/Organic_matter/t17tVCvk">organic matter</a> requires a suite of extracellular enzymes to access the carbon and nutrients embedded in <a href="/facts/Detritus/8IjhrXA6">detritus</a>. Microorganisms differ in their ability to break down these different substrates and few organisms have the potential to degrade all the available plant cell wall materials.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> To detect the presence of complex polymers, some exoenzymes are produced constitutively at low levels, and expression is <a href="/facts/Upregulated/6nRoa28r">upregulated</a> when the substrate is abundant.<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> This sensitivity to the presence of varying concentrations of substrate allows fungi to respond dynamically to the changing availability of specific resources. Benefits of exoenzyme production can also be lost after secretion because the enzymes are liable to denature, degrade or diffuse away from the producer cell. </p><p>Enzyme production and secretion is an energy intensive process<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> and, because it consumes resources otherwise available for reproduction, there is evolutionary pressure to conserve those resources by limiting production.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> Thus, while most microorganisms can assimilate simple monomers, degradation of polymers is specialized, and few organisms can degrade recalcitrant polymers like cellulose and lignin.<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> Each microbial species carries specific combinations of <a href="/facts/Genes/e1swwPY6">genes</a> for extracellular enzymes and is adapted to degrade specific <a href="/facts/Substrate_(biology)/EBDd458H">substrates</a>.<a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a> In addition, the expression of genes that encode for enzymes is typically regulated by the availability of a given substrate. For example, presence of a low-molecular weight soluble substrate such as glucose will inhibit enzyme production by repressing the transcription of associated cellulose-degrading enzymes.<a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a> </p><p>Environmental conditions such as <a href="/facts/Soil_pH/D9G9ChcT">soil pH</a>,<a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> soil temperature,<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a> moisture content,<a class="footnote-ref" id="fnref:23" href="#fn:23"><sup>23</sup></a> and plant litter type and quality<a class="footnote-ref" id="fnref:24" href="#fn:24"><sup>24</sup></a> have the potential to alter exoenzyme expression and activity. Variations in seasonal temperatures can shift metabolic needs of microorganisms in synchrony with shifts in plant nutrient requirements.<a class="footnote-ref" id="fnref:25" href="#fn:25"><sup>25</sup></a> Agricultural practices such as fertilizer amendments and tillage can change the spatial distribution of resources, resulting in altered exoenzyme activity in the <a href="/facts/Soil_profile/GcXhdams">soil profile</a>.<a class="footnote-ref" id="fnref:26" href="#fn:26"><sup>26</sup></a> Introduction of moisture exposes <a href="/facts/Soil_organic_matter/WrAuRGp4">soil organic matter</a> to enzyme catalysis<a class="footnote-ref" id="fnref:27" href="#fn:27"><sup>27</sup></a> and also increases loss of soluble monomers via diffusion. Additionally, osmotic shock resulting from water potential changes can impact enzyme activities as microbes redirect energy from enzyme production to synthesizing <a href="/facts/Osmolyte/Cdxr1uj9">osmolytes</a> to maintain cellular structures. </p> <h2 id="extracellular-enzyme-activity-in-fungi-during-plant-decomposition">Extracellular enzyme activity in fungi during plant decomposition</h2> <p>Most of the extracellular enzymes involved in polymer degradation in leaf litter and soil have been ascribed to fungi.<a class="footnote-ref" id="fnref:28" href="#fn:28"><sup>28</sup></a><a class="footnote-ref" id="fnref:29" href="#fn:29"><sup>29</sup></a><a class="footnote-ref" id="fnref:30" href="#fn:30"><sup>30</sup></a> By adapting their metabolism to the availability of varying amounts of carbon and nitrogen in the environment, fungi produce a mixture of oxidative and hydrolytic enzymes to efficiently break down lignocelluloses like wood. During plant litter degradation, cellulose and other labile substrates are degraded first<a class="footnote-ref" id="fnref:31" href="#fn:31"><sup>31</sup></a> followed by lignin depolymerization with increased oxidative enzyme activity and shifts in microbial community composition. </p><p>In plant cell walls, cellulose and hemicellulose is embedded in a pectin scaffold<a class="footnote-ref" id="fnref:32" href="#fn:32"><sup>32</sup></a> that requires pectin degrading enzymes, such as <a href="/facts/Polygalacturonase/lw0VvcKR">polygalacturonases</a> and <a href="/facts/Pectin_lyase/2e8QTG29">pectin lyases</a> to weaken the plant cell wall and uncover hemicellulose and cellulose to further enzymatic degradation.<a class="footnote-ref" id="fnref:33" href="#fn:33"><sup>33</sup></a> Degradation of lignin is catalyzed by enzymes that oxidase aromatic compounds, such as <a href="/facts/Phenol_oxidase/9vJr5m2c">phenol oxidases</a>, <a href="/facts/Peroxidases/pEgHpmCV">peroxidases</a> and laccases. Many fungi have multiple genes encoding lignin-degrading exoenzymes.<a class="footnote-ref" id="fnref:34" href="#fn:34"><sup>34</sup></a> </p><p>Most efficient wood degraders are <a href="/facts/Saprotrophic/sJkDfrJW">saprotrophic</a> <a href="/facts/Ascomycetes/4GJdsf2e">ascomycetes</a> and <a href="/facts/Basidiomycetes/LuFeC7D2">basidiomycetes</a>. Traditionally, these fungi are classified as <a href="/facts/Wood-decay_fungus/UHRCmnQ8">brown rot</a> (Ascomycota and Basidiomycota), white rot (Basidiomycota) and soft rot (Ascomycota) based on the appearance of the decaying material.<a class="footnote-ref" id="fnref:35" href="#fn:35"><sup>35</sup></a> Brown rot fungi preferentially attack cellulose and hemicellulose;<a class="footnote-ref" id="fnref:36" href="#fn:36"><sup>36</sup></a> while white rot fungi degrade cellulose and lignin. To degrade cellulose, basidiomycetes employ hydrolytic enzymes, such as <a href="/facts/Endoglucanase/B5ppt817">endoglucanases</a>, <a href="/facts/Cellulase/B5ppt817">cellobiohydrolase</a> and β-glucosidase.<a class="footnote-ref" id="fnref:37" href="#fn:37"><sup>37</sup></a> Production of endoglucanases is widely distributed among fungi and cellobiohydrolases have been isolated in multiple white-rot fungi and in plant pathogens.<a class="footnote-ref" id="fnref:38" href="#fn:38"><sup>38</sup></a> β-glucosidases are secreted by many wood-rotting fungi, both white and brown rot fungi, <a href="/facts/Mycorrhiza/bAqxvRwm">mycorrhizal</a> fungi<a class="footnote-ref" id="fnref:39" href="#fn:39"><sup>39</sup></a> and in plant pathogens. In addition to cellulose, β-glucosidases can cleave xylose, mannose and galactose.<a class="footnote-ref" id="fnref:40" href="#fn:40"><sup>40</sup></a> </p><p>In white-rot fungi such as <i><a href="/facts/Phanerochaete_chrysosporium/UKk4PSL5">Phanerochaete chrysosporium</a></i>, expression of manganese-peroxidase is induced by the presence of manganese, hydrogen peroxide and lignin,<a class="footnote-ref" id="fnref:41" href="#fn:41"><sup>41</sup></a> while laccase is induced by availability of phenolic compounds.<a class="footnote-ref" id="fnref:42" href="#fn:42"><sup>42</sup></a> Production of lignin-peroxidase and manganese-peroxidase is the hallmark of basidiomycetes and is often used to assess basidiomycete activity, especially in biotechnology applications.<a class="footnote-ref" id="fnref:43" href="#fn:43"><sup>43</sup></a> Most white-rot species also produce laccase, a copper-containing enzyme that degrades polymeric lignin and <a href="/facts/Humic/nU58wtUm">humic</a> substances.<a class="footnote-ref" id="fnref:44" href="#fn:44"><sup>44</sup></a> </p><p>Brown-rot basidiomycetes are most commonly found in coniferous forests, and are so named because they degrade wood to leave a brown residue that crumbles easily. Preferentially attacking hemicellulose in wood, followed by cellulose, these fungi leave lignin largely untouched.<a class="footnote-ref" id="fnref:45" href="#fn:45"><sup>45</sup></a> The decayed wood of soft-rot Ascomycetes is brown and soft. One soft-rot Ascomycete, <i><a href="/facts/Trichoderma_reesei/rKXo5PTp">Trichoderma reesei</a></i>, is used extensively in industrial applications as a source for cellulases and hemicellulases.<a class="footnote-ref" id="fnref:46" href="#fn:46"><sup>46</sup></a> Laccase activity has been documented in <i>T. reesei</i>, in some species in the <a href="/facts/Aspergillus/pKhecLTW">Aspergillus</a> <a href="/facts/Genus/m8EFjSms">genus</a><a class="footnote-ref" id="fnref:47" href="#fn:47"><sup>47</sup></a> and in freshwater ascomycetes.<a class="footnote-ref" id="fnref:48" href="#fn:48"><sup>48</sup></a> </p> <h2 id="measuring-fungal-extracellular-enzyme-activity-in-soil-plant-litter-and-other-environmental-samples">Measuring fungal extracellular enzyme activity in soil, plant litter, and other environmental samples</h2> <p>Methods for estimating soil enzyme activities involve sample harvesting prior to analysis, mixing of samples with buffers and the use of substrate. Results can be influenced by: sample transport from field-site, storage methods, pH conditions for <a href="/facts/Assay/fPUYjx1I">assay</a>, substrate concentrations, temperature at which the assay is run, sample mixing and preparation.<a class="footnote-ref" id="fnref:49" href="#fn:49"><sup>49</sup></a> </p><p>For hydrolytic enzymes, colorimetric assays are required that use a <a href="/facts/P-nitrophenol/u2AXK9aN">p-nitrophenol</a> (p-NP)-linked substrate,<a class="footnote-ref" id="fnref:50" href="#fn:50"><sup>50</sup></a> or <a href="/facts/Fluorometric/mBcweHKk">fluorometric</a> assays that use a 4-methylumbelliferone (MUF)-linked substrate.<a class="footnote-ref" id="fnref:51" href="#fn:51"><sup>51</sup></a> </p><p>Oxidative enzymes such as phenol oxidase and peroxidase mediate lignin degradation and humification.<a class="footnote-ref" id="fnref:52" href="#fn:52"><sup>52</sup></a> Phenol oxidase activity is quantified by oxidation of L-3, 4-dihydoxyphenylalanine (L-DOPA), <a href="/facts/Pyrogallol/j2TQ16hT">pyrogallol</a> (1, 2, 3-trihydroxybenzene), or <a href="/facts/ABTS/v9qUAIMK">ABTS</a> (2, 2’-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid). Peroxidase activity is measured by running the phenol oxidase assay concurrently with another assay with L-DOPA and hydrogen peroxide (H2O2) added to every sample.<a class="footnote-ref" id="fnref:53" href="#fn:53"><sup>53</sup></a> The difference in measurements between the two assays is indicative of peroxidase activity. Enzyme assays typically apply proxies that reveal exo-acting activities of enzymes. Exo-acting enzymes hydrolyze substrates from the terminal position. While activity of endo-acting enzymes which break down polymers midchain need to be represented by other substrate proxies. New enzyme assays aim to capture the diversity of enzymes and assess the potential activity of them in a more clear way.<a class="footnote-ref" id="fnref:54" href="#fn:54"><sup>54</sup></a><a class="footnote-ref" id="fnref:55" href="#fn:55"><sup>55</sup></a><a class="footnote-ref" id="fnref:56" href="#fn:56"><sup>56</sup></a> </p><p>With newer technologies available, molecular methods to quantify abundance of enzyme-coding genes are used to link enzymes with their producers in soil environments.<a class="footnote-ref" id="fnref:57" href="#fn:57"><sup>57</sup></a><a class="footnote-ref" id="fnref:58" href="#fn:58"><sup>58</sup></a> Transcriptome analyses are now employed to examine genetic controls of enzyme expression,<a class="footnote-ref" id="fnref:59" href="#fn:59"><sup>59</sup></a> while <a href="/facts/Proteomic/3aqQ1tFh">proteomic</a> methods can reveal the presence of enzymes in the environment and link to the organisms producing them.<a class="footnote-ref" id="fnref:60" href="#fn:60"><sup>60</sup></a> </p> <table><tbody><tr><th>Process</th><th>Enzyme</th><th>Substrate</th></tr><tr><td>Cellulose-degradation</td><td>Cellobiohydrolase<p>β-glucosidase</p></td><td>pNP, MUF<a class="footnote-ref" id="fnref:61" href="#fn:61"><sup>61</sup></a><a class="footnote-ref" id="fnref:62" href="#fn:62"><sup>62</sup></a></td></tr><tr><td>Hemicellulose-degradation</td><td>β-glucosidases<p>Esterases </p></td><td>pNP, MUF<a class="footnote-ref" id="fnref:63" href="#fn:63"><sup>63</sup></a><a class="footnote-ref" id="fnref:64" href="#fn:64"><sup>64</sup></a></td></tr><tr><td>Polysaccharide-degradation</td><td>α-glucosidases<p>N-acetylglucosaminidase</p></td><td>pNP, MUF<a class="footnote-ref" id="fnref:65" href="#fn:65"><sup>65</sup></a></td></tr><tr><td>Lignin-degradation</td><td>Mn-peroxidase<p>Laccase (polyphenol oxidase)</p><p>Peroxidase </p></td><td>Pyrogallol, L-DOPA, ABTS<a class="footnote-ref" id="fnref:66" href="#fn:66"><sup>66</sup></a><p>L-DOPA, ABTS<a class="footnote-ref" id="fnref:67" href="#fn:67"><sup>67</sup></a></p></td></tr></tbody></table> <h2 id="applications-of-fungal-extracellular-enzymes">Applications of fungal extracellular enzymes</h2> <table><tbody><tr><th>Application</th><th>Enzymes & their uses</th></tr><tr><td>Paper production</td><td>Cellulases – improve paper quality and smooth fibers<a class="footnote-ref" id="fnref:68" href="#fn:68"><sup>68</sup></a><p>Laccases – soften paper and improving bleaching<a class="footnote-ref" id="fnref:69" href="#fn:69"><sup>69</sup></a></p></td></tr><tr><td>Biofuel generation</td><td>Cellulases – for production of renewable liquid fuels<a class="footnote-ref" id="fnref:70" href="#fn:70"><sup>70</sup></a></td></tr><tr><td>Dairy industry</td><td>Lactase – part of β-glucosidase family of enzymes and can break down lactose to glucose and galactose<p>Pectinases – in the manufacture of <a href="/facts/Yogurt/JoQjepa7">yogurt</a></p></td></tr><tr><td>Brewing industry</td><td>Beer production and malting<a class="footnote-ref" id="fnref:71" href="#fn:71"><sup>71</sup></a></td></tr><tr><td>Fruit and jam manufacturing</td><td>Pectinases, cellulases – to clarify fruit juices and form jams</td></tr><tr><td><a href="/facts/Bioremediation/zft68Ez9">Bioremediation</a></td><td>Laccases – as biotransformers to remove nonionic <a href="/facts/Surfactants/zgVX6g8o">surfactants</a><a class="footnote-ref" id="fnref:72" href="#fn:72"><sup>72</sup></a><a class="footnote-ref" id="fnref:73" href="#fn:73"><sup>73</sup></a></td></tr><tr><td>Waste water treatment</td><td>Peroxidases - removal of pollutants by precipitation<a class="footnote-ref" id="fnref:74" href="#fn:74"><sup>74</sup></a><a class="footnote-ref" id="fnref:75" href="#fn:75"><sup>75</sup></a></td></tr><tr><td>Sludge treatment</td><td><a href="/facts/Lipase/nPgIyNBS">Lipases</a> - used in degradation of particulate organic matter<a class="footnote-ref" id="fnref:76" href="#fn:76"><sup>76</sup></a></td></tr><tr><td>Phytopathogen management</td><td>Hydrolytic enzymes produced by fungi, e.g. <i>Fusarium graminearum</i>, pathogen on cereal grains resulting in economic losses in agriculture <a class="footnote-ref" id="fnref:77" href="#fn:77"><sup>77</sup></a></td></tr><tr><td>Resource management<p>Water retention</p></td><td>Soil aggregates and water infiltration influence enzyme activity<a class="footnote-ref" id="fnref:78" href="#fn:78"><sup>78</sup></a><a class="footnote-ref" id="fnref:79" href="#fn:79"><sup>79</sup></a></td></tr><tr><td>Soil fertility and plant production</td><td>Use of enzyme activity as indicator of soil quality<a class="footnote-ref" id="fnref:80" href="#fn:80"><sup>80</sup></a><a class="footnote-ref" id="fnref:81" href="#fn:81"><sup>81</sup></a></td></tr><tr><td><a href="/facts/Compost/q6kmXGWU">Composting</a></td><td>Impacts of composting municipal solid waste on soil microbial activity<a class="footnote-ref" id="fnref:82" href="#fn:82"><sup>82</sup></a></td></tr><tr><td>Soil organic matter stability</td><td>Impact of temperature and soil respiration on enzymatic activity and its effect on soil fertility<a class="footnote-ref" id="fnref:83" href="#fn:83"><sup>83</sup></a></td></tr><tr><td>Climate change indicators<p>Impact on soil processes</p></td><td>Potential increase in enzymatic activity leading to elevated CO2 emissions<a class="footnote-ref" id="fnref:84" href="#fn:84"><sup>84</sup></a></td></tr><tr><td>Quantifying <a href="/facts/Global_warming/rEN4BDE7">global warming</a> outcomes</td><td>Predictions based on soil organic matter decomposition<a class="footnote-ref" id="fnref:85" href="#fn:85"><sup>85</sup></a> and strategies for mitigation<a class="footnote-ref" id="fnref:86" href="#fn:86"><sup>86</sup></a></td></tr><tr><td>Impact of elevated CO2 on enzyme activity & decomposition</td><td>Understanding the implication of microbial responses and its impact on terrestrial ecosystem functioning<a class="footnote-ref" id="fnref:87" href="#fn:87"><sup>87</sup></a></td></tr></tbody></table> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Enzymes/DSI1Fh7y">Enzymes</a></li> <li><a href="/facts/Enzyme_kinetics/LJ0lWoMc">Enzyme kinetics</a></li> <li><a href="/facts/Enzyme_assay/3SHu9GkN">Enzyme assay</a></li> <li><a href="/facts/List_of_enzymes/w2RP6EwU">List of enzymes</a></li> <li><a href="/facts/Decomposition/6Bve4pgl">Decomposition</a></li> <li><a href="/facts/Plant_litter/Y0aJpt4P">Plant litter</a></li> <li><a href="/facts/Nutrient_cycle/S57nuGbQ">Nutrient cycle</a></li></ul> <h2 id="further-reading">Further reading</h2> <ul><li><a href="http://www.chem.qmul.ac.uk/iubmb/enzyme/">Enzyme nomenclature</a></li> <li><a href="https://web.archive.org/web/20121228002422/http://www.emc.maricopa.edu/faculty/farabee/biobk/biobookenzym.html">Reactions and enzymes</a></li> <li>Richard P. Dick (ed.) 2011. Methods in Soil Enzymology. <i>Soil Science Society of America</i>, Wisconsin, USA <a href="/facts/ISBN_(identifier)/15AdSPa9">ISBN</a> 978-0-89118-854-4</li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://www.enzyme-database.org">ExplorEnz</a>- searchable enzyme database to access the IUBMB Enzyme Nomenclature List</li> <li><a href="http://www.brenda-enzymes.org">BRENDA</a> – database and related literature of known enzymes</li> <li><a href="http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/enzyme">Enzyme structures</a></li> <li><a href="http://enzyme.expasy.org">ExPASy</a> database for sequence data</li> <li><a href="http://www.genome.jp/kegg">KEGG: Kyoto Encyclopedia of Genes and Genomes</a> biochemical pathways and enzymes database</li> <li><a href="https://mycoclap.fungalgenomics.ca/mycoCLAP/">MycoCLAP</a> searchable database of fungal enzyme genes</li> <li><a href="http://metacyc.org">MetaCyc</a> metabolic pathways of different organisms</li> <li><a href="http://pec.biodbs.info">Pectinase</a> <a href="https://web.archive.org/web/20190915075210/http://pec.biodbs.info/">Archived</a> 2019-09-15 at the <a href="/facts/Wayback_Machine/nmQ3a6JC">Wayback Machine</a> database for pectinase enzymes and their inhibitors</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Sinsabaugh, R. 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