Fungal accessory enzymes for the cleavage of hemicellulose-derived residues.
The search for renewable sources of energy requires a worldwide effort in order to decrease the harmful effects of global climate change, as well as to satisfy the future energy demands. In this context, biofuels are emerging as a new source of energy derived from biomass. The production of biofuels could decrease effectively the impact of pollutants in the atmosphere, in addition to assisting in the management for tons of biomass waste. Biomass (plant matter) can be referred to "traditional biomass", which is used in inefficient ways such as the highly pollutant primitive cooking stoves (wood), and "modern biomass" that refers to biomass produced in a sustainable way and used for electricity generation, heat production and transportation of liquid fuels . In addition to these definitions, The International Energy Agency (IEA) defines biomass as any plant matter that could be used directly as fuel or converted into fuels, electricity or heat. Therefore, in order to provide useful management of biomass, it is clear that one needs to learn how to extract energy from plants.
Plant cells are mainly composed by lignocellulosic material, which includes cellulose, hemicellulose and lignin (lignocellulosic complex). The hydrolysis of lignocellulose to glucose is a major bottleneck in cellulosic biofuel production processes . In nature, microorganisms, especially fungi, are able to degrade the plant cell wall through a set of acting synergistically enzymes. This phenomenon leads to glucose being released in a free form, which can enter the metabolism of the microorganism, providing its energy. A great challenge is to modify the architecture of the plant cell walls and/or the ability of the microorganisms to degrade it, by modifying their genomes. For instance, researchers can generate genetically engineered microorganisms able to degrade efficiently the polymers in the plant cells, producing sugars monomers that can be fermented directly by yeasts, generating ethanol. This chapter will describe the composition of plant cell walls and how microorganisms cope with the lignocellulosic material. The main focus will be on fungi cell wall degrading enzymes (CWDEs) and their genetic regulation. The aim of this chapter is to guide scientists in order to genetically improve microorganisms that can be able to efficiently degrade the plant biomass. Also, new strains could be great producers of CWDEs, providing enzymatic cocktails that can be introduced commercially. Finally, the future perspectives will demonstrate how far we are from cellulosic ethanol and other biomass-derived chemical compounds, regarding to research of microorganisms.
2. Plant cell wall polysaccharides and lignin
Plant cell wall  polysaccharides are the most abundant organic compounds found in nature. These compounds consist mainly of polysaccharides such as cellulose, hemicelluloses and pectin, as well as the phenolic polymer lignin. Together, the polysaccharides and lignin provide high complexity and rigidity to the plant cell wall. Cellulose, the major constituent of plant cell wall consists of ß-1,4 linked D-glucose units that form linear polymeric chains of about 8000-12 000 glucose units. In its crystalline form, cellulose consists of chains that are packed together by hydrogen bonds to form highly insoluble structures, called microfibrils. In addition to the crystalline structure, cellulose contains amorphous regions within the microfibrils (noncrystalline structure) .
Hemicelluloses are heterogeneous polysaccharides consisted by different units of sugars, being the second most abundant polysaccharides in plant cell wall. Hemicelluloses are usually classified according to the main residues of sugars present in the backbone of the structural polymer. Xylan, the most abundant hemicellulose polymer in cereals and hardwood, is composed by ß-1,4-linked D-xylose units in the main backbone, and can be substituted by different side groups such as D-galactose, L-arabinose, glucuronic acid, acetyl, feruloyl, and
Pectins are another family of plant cell wall heteropolysaccharides, containing a backbone of α-1,4-linked D-galacturonic acid. The polymers usually contain two different types of regions. The so-called "smooth" region of pectins contains residues of D-galacturonic acids that can be methylated or acetylated. In the other region, referred as "hairy" region, the backbone of D-galacturonic acids residues is interrupted by α-1,2-linked L-rhamnose residues. In the hairy region, long side chains of L-arabinose and D-galactose residues can be attached to the rhamnose residues . Figure 2 depicts a schematic representation of the hairy region of pectins.
Lignin is a phenolic polymer that confers strength to plant cell wall. Lignin is a highly insoluble complex branched polymer of substituted phenylpropane units, which are joined together by ether and carbon-carbon linkages, forming an extensive cross-linked network within the cell wall. The cross-linking between the different polymers described above confers the complexity and rigidity of the plant cell wall, which is responsible for the protection of plant cell as a whole. In addition to offer protection against mechanical stress and osmotic lysis, the plant cell wall is an effective barrier against pathogens, including many microorganisms. However, during the course of evolution some microorganisms, in order to survive, developed efficient strategies to degrade plant cell wall components, mainly the polysaccharides .
Plant cell wall degradation mechanisms are pivotal for the lifestyle of many microorganisms, once they should be able to degrade the plant polymers to acquire nutrients from plants. For instance, saprophytic fungi inhabit dead organic materials like decaying wood and leaves. In order to take energy from these materials, these fungi need to produce enzymes capable of degrading the majority of plant cell wall polysaccharides present in the biomass. The main mechanism through which fungi and other microorganisms degrade plant biomass consists of production and secretion of enzymes acting synergistically in the plant cell wall, releasing monomers that can be used by the microorganism as chemical energy. The next section will discuss mechanisms of cell wall degrading enzymes (CWDE) production by fungi, the most important producers of carbohydrate-active enzymes.
3. Microbial degradation of plant cell wall polysaccharides
In order to survive, microorganisms developed, during the course of evolution, physiological mechanisms to cope with a variety of environmental factors. The acquirement of nutrients represents a challenge for all living organisms, especially for microorganisms. Saprophytism, one of the most common lifestyle of microorganisms, involves living in dead or decaying organic matter, mainly composed by plant biomass. In this context, microorganisms developed cellular mechanisms in order to take energy from plant biomass, and one of this mechanisms involves the production and secretion of carbohydrate-active enzymes. These enzymes degrade the plant cell wall, releasing sugars monomers that can be used as substrates for the metabolism of the microorganism. The microbial use of plant biomass is pivotal for life on Earth, because it is responsible for large portions of carbon flux in the biosphere. In addition, plant cell wall-degrading enzymes (CWDEs) have a broad range of industrial applications, such as within the food and feed industry and for sustainable production of many chemicals and fuels.
The capacity to degrade lignocellulose is mainly distributed among fungi and bacteria. Cellulolytic bacteria can be found in different genus such as
Concerning to lignin degradation, many white-rot basidiomycetes and some actinomycetes are able to produce lignin-degrading enzymes, especially peroxidases. For instance,
The plant cell wall-degrading machinery of aerobic and anaerobic microorganisms differs significantly, regarding to its macromolecular organization. The cellulase/hemicellulase apparatus of anaerobic bacteria is frequently assembled into a large multienzyme complex, named cellulosomes [14, 15]. This complex contains enzymes with a variety of activities such as polysaccharide lyases, carbohydrate esterases and glycoside hydrolases [16-18]. Basically, the catalytic components of the cellulosomes include a structure named dockerins, which are noncatalytic modules that bind to cohesin modules, located in a large noncatalytic protein acting as scaffold . The protein-protein interaction between dockerins and cohesins allows the integration of the hydrolytic enzymes into the complex [19, 20]. It has been demostrated that scaffoldins are also responsible for the anchoring of the whole complex onto crystalline cellulose, through a noncatalytic carbohydrate-binding module (CBM) . The main studies concerning cellulosomes are being focused on anaerobic bacteria, especially from
4. Ethanol production from the fermentable feedstock from lignocellulosic biomass
Fermentative production of ethanol is largely performed nowadays through the use of starch or sucrose provided by agricultural crops such as wheat, corn or sugarcane. In Brazil, for instance, the ethanol production through yeast fermentation of substrates from sugarcane is a well-known and consolidated process. However, the improvement of fermentative processes towards utilization of lower-value substrates such as lignocellulosic residues is emerging as a valuable approach for reducing the production cost and consequently increasing the use of ethanol as biofuel. In sugarcane mills, for instance, a large quantity of sugarcane bagasse, which is a great source of lignocellulosic residue, is produced as a by-product of the industrial process. The sugarcane bagasse can be used as a lower-value substrate to produce the so-called second generation ethanol, in other words the ethanol generated from lignocellulosic material. The conversion of lignocellulose to ethanol requires challenging biological processes that includes: (i) delignification in order to release free cellulose and hemicellulose from the lignocellulosic material; (ii) depolymerization of the carbohydrates polymers from the cellulose and hemicellulose to generate free sugars; and (iii) fermentation of mixed hexose and pentose sugars to finally produce ethanol . Glucose presents approximately 60% of the total sugars available in cellulosic biomass. The yeast
In summary, many microorganisms are able to produce and secrete hemicellulolytic enzymes, but fungi are pointed as the most important microorganisms concerning the biomass degradation. The significance of secreted enzymes in the life of these organisms and the biotechnological importance of filamentous fungi and their enzymes prompted an interest towards understanding the mechanisms of expression and regulation of the extracellular enzymes, as well as the characterization of the transcription factors involved. The next sections of this chapter will discuss the fungal enzyme sets for lignocellulosic degradation and the gene expression regulation of these enzymes.
5. Fungal enzyme sets for lignocellulosic degradation
Fungi play a central role in the degradation of plant biomass, producing an extensive array of carbohydrate-active enzymes responsible for polysaccharide degradation. The enzyme sets for plant cell wall degradation differ between many fungal species, and our understanding about fungal diversity with respect to degradation of plant matter is essential for the improvement of new strains and the development of enzymatic cocktails for industrial applications.
Carbohydrate-active enzymes are usually classified in different families, based on amino acid sequence of the related catalytic module. An extensive and detailed database presenting these hydrolytic enzymes can be found at www.cazy.org (CAZymes,
6. Cellulose degradation
Cellulose, a polysaccharide consisted of linear β-1,4-linked D-glucopyranose chains, requires three classes of enzymes for its degradation: β-1,4-endoglucanases (EGL), exoglucanases/cellobiohydrolases (CBH), and β-glucosidase (BGL). The endoglucanases cleave cellulose chains internally mainly from the amorphous region, releasing units to be degraded by CBHs and/or BGLs. The cellobiohydrolases cleave celobiose units (the cellulose-derived disaccahride) from the end of the polysaccharide chains . Finally, β-glucosidases hydrolise cellobiose to glucose, the monomeric readily metabolisable carbon source for fungi . These three classes of enzymes need to act synergistically and sequentially in order to degrade completely the cellulose matrix. After endo- and exo-cleaving (performed by EGLs and CBHs, respectively), the BGLs degrade the remaining oligosaccharides to glucose. A schematic view of cellulose degradation is depicted in the Figure 3.
The most efficient cellulose-degrading fungi is
7. Hemicellulose degradation
Hemicellulose is a complex polysaccharide matrix composed of different residues branched in three kinds of backbones, named xylan, xyloglucan and mannan. The complexity of hemicellulose requires a concerted action of endo-enzymes cleaving internally the main chain, exo-enzymes releasing monomeric sugars, and accessory enzymes cleaving the side chains of the polymers or associated oligosaccharides, leading to the release of various mono- and disaccharides depending on hemicellulose type.
Xylan, a polymer composed by ß-1,4-linked D-xylose units, is degraded through the action of ß-1,4-endoxylanase, which cleaves the xylan backbone into smaller oligosaccharides, and ß-1,4-xylosidase, which cleaves the oligosaccharides into xylose. Fungal ß-1,4-endoxylanase are classified as GH10 or GH11 , differing from each other in substrate specificty . Endoxylanases belonging to family GH10 usually have broader substrate specificity than endoxylanases from family GH11 . GH10 endoxylanases are known to degrade xylan backbones with a high degree of substitutions and smaller xylo-oligosaccharides in addition to degrade linear chains of 1,4-linked D-xylose residues. Thus, GH10 endoxylanases are necessary to degrade completely substituted xylans . ß-Xylosidases are highly specific for small unsubstituted xylose olygosaccharides and they are important for the complete degradation of xylan. Some ß-xylosidases have been shown transxylosylation activity, suggesting a role for these enzymes in the synthesis of specific oligosaccharides [43, 44].
Xyloglucan consists of ß-1,4-linked D-glucose backbone substituted mainly by D-xylose and therefore requires endoglucanases (xyloglucanases) and ß-glucosidases action in order to be degraded. Some endoglucanases are specific for the substituted xyloglucan backbone, and they are not able to hydrolise cellulose . Xyloglucan-active endoglucanases have specific modes of action. For instance, a xyloglucanase from
Mannans, also referred to galacto(gluco)mannans, consist of a backbone of ß-1,4-linked D-mannose (mannans) and D-glucose (glucomannans) residues with D-galactose side chains. The degradation of this type of hemicellulose is performed by the action of ß-endomannanases (ß-mannanases) and ß-mannosidases, commonly expressed by aspergilli . The ß-mannanases cleave the backbone of galacto(gluco)mannans, releasing mannooligosaccharides. Several structural features in the polymer determine the ability of ß-mannanases to hydrolise the mannan backbone, such as the ratio of glucose to mannose and the number and distribution of substituents on the backbone . It has been shown that ß-mannanase is most active on galactomannans with a low substitution of the backbone , and the presence of galactose residues on the mannan backbone significantly prevents ß-mannanase activity . The main products of ß-mannanase activity on mannan are mannobiose and mannotriose. ß-Mannosidases act on the nonreducing ends of mannooligosaccharides, releasing mannose. As shown by substrate specificity studies, ß-Mannosidase is able to completely release terminal mannose residues when one or more adjacent unsubstituted mannose residues are present .
The complete degradation of hemicellulose is only achieved after release of all substitutions present on the main backbone. The high degree of substitution in the hemicellulose polymers requires the action of various accessory enzymes able to release all these substitutions from the polysaccharide. At least nine different enzyme activities distributed along 12 GH and 4 CE families are required to completely degrade the hemicellulose substituents .
Arabinose is one of the most common sugar residues in hemicellulose and is present in arabinose-substituted xyloglucan and (arabino-)xylan. The release of arabinose from the polymer is performed by α-arabinofuranosidases and arabinoxylan arabinofuranohydrolases. α-Arabinofuranosidases are mainly found in GH 51 and 54 families, and the differences in the substrate specificity between these enzymes could be exemplified by two arabinofuranosidases of
Another type of substituent present in hemicellulose is D-xylose. Hydrolases responsible for the release of D-xylose residues from the xyloglucan backbone are referred to α-xylosidases. These enzymes can differ with respect to the type of glycoside they can hydrolize. For instance, α-xylosidase II (AxhII) from
There are many other possible substituents in hemicellulose, such as L-fucose, α-linked D-galactose, D-glucuronic acid, acetyl group and
|Xylan||acetyl group||acetyl xylan esterases|
|Xylan||ferulic acid||feruloyl esterases|
8. Pectin degradation
Pectins are composed of a main backbone of α-1,4-linked D-galacturonic acid, and consist of two regions: the "smooth" region and the "hairy" region. The "smooth” region contains residues of D-galacturonic acids that can be methylated or acetylated, while in the "hairy" region, the backbone of D-galacturonic acids residues is interrupted by α-1,2-linked L-rhamnose residues. Moreover, in the hairy region, long side chains of L-arabinose and D-galactose residues can be attached to the rhamnose residues (Figure 2). As observed for cellulose and hemicellulose, degradation of pectins also requires a set of hydrolytic enzymes to degrade completely the polymer. Glycoside hydrolases (GHs) and polysaccharide lyases (PLs) are the two classes of hydrolytic enzymes required for pectin backbone degradation.
The GHs involved in pectin backbone degradation include endo- and exo-polygalacturonases, which cleave the backbone of smooth regions, while the intricate hairy regions are further degraded by endo- and exo-rhamnogalacturonases, xylogalacturonases, α-rhamnosidases, unsaturated glucuronyl hydrolases, and unsaturated rhamnogalacturonan hydrolases . Endo- and exo-polygalacturonases are able to cleave α-1,4-glycosidic bonds of α-galacturonic acids. Rhamnogalacturonases cleave α-1,2-glycosidic bonds between D-galacturonic acid and L-rhamnose residues in the hairy region of the pectin backbone . An endo-xylogalacturonase from
The fungal PLs pectin and pectate lyases hydrolyze α-1,4-linked D-galacturonic acid residues in the smooth regions of pectin backbone . Pectin lyases have preference for substrates with a high degree of methylesterification, whereas pectate lyases prefer substrates with a low degree of esterification. Moreover, pectate lyases require Ca2+ ions for catalysis while pectin lyases lack such ion requirement to catalysis . The PL rhamnogalacturonan lyase cleaves within the hairy region of pectin and appears to be structurally different from pectin and pectate lyases. As presented by nailing reviews [33, 48], the pectin structures xylogalacturonan and rhamnogalacturonan require a repertoire of accessory enzymes to remove the side chains, providing access for the main-chain pectinolytic enzymes. The accessory enzymes endoarabinanases, exoarabinanases, β-endogalactanases, and several esterases are specific for pectin degradation, while α-arabinofuranosidases, β-galactosidases, and β-xylosidases are also required for hemicellulose degradation.
9. Lignin degradation
Lignin, a highly insoluble complex branched polymer of substituted phenylpropane units joined by carbon-carbon and ether linkages, provides an extensive cross-linked network within the cell wall, and it is known to increase the strength and recalcitrance of the plant cell wall. Microbial lignin degradation is often complicated, once the microbe needs to cope with three major challenges related to lignin structure: (i) enzymatic system to degrade the lignin polymer needs to be essentially extracellular, because lignin is a large polymer, (ii) the mechanism of enzymatic degradation should be oxidative and not hydrolytic, since the lignin structure comprises carbon-carbon and ether bonds, and (iii) lignin stereochemistry is irregular, requiring enzymes with less specificity than hydrolytic enzymes required for cellulose/hemicellulose degradation . The most well characterized enzymes able to degrade the lignin polymer are lignin peroxidase (LiP), laccase (Lac), manganese peroxidase (MnP), versatile peroxidase, and H2O2-generating enzymes such as glyoxal oxidase (GLOX) and aryl alcohol oxidase (AAO).
Lignin and manganese peroxidases (LiP and MnP, respectively) catalyse a variety of oxidative reactions dependent on H2O2. LiP oxidizes non-phenolic units of lignin (mainly Cα-Cβ bonds) by removing one electron and creating cation radicals that decompose chemically . MnPs differ significantly from LiPs, once they cannot oxidize directly non-phenolic lignin-related structures . In order to oxidize non-phenolic lignin-related components, the oxidizing power of MnPs is transferred to Mn3+, a product of the MnP reaction: 2 Mn(II) + 2H+ + H2O2 → 2 Mn(III) + 2H2O . In this way, Mn3+ diffuses into the lignified cell wall, attacking it from the inside .
Laccases oxidize phenolic compounds and reduce molecular oxygen to water. Lac catalyses the formation of phenoxyl radicals and their unspecific reactions, leading finally to Cα-hydroxyl oxidation to ketone, alkyl-aryl cleavage, demethoxylation and Cα-Cβ cleavage in phenolic substructures . Versatile peroxidases (VPs) are able to oxidize phenolic and non-phenolic aromatic compounds, as well as Mn2+ .
In order to degrade lignin, microbes require sources of extracellular H2O2, to support the oxidative turnover of LiPs and MnPs responsible for ligninolysis. The hydrogen peroxide is provided by extracellular oxidases that reduce molecular oxygen to H2O2, with the synergistic oxidation of a cosubstrate. The most well characterized extracellular H2O2-generating enzymes are glyoxal oxidase (GLOX) and aryl alcohol oxidase (AAO).
Most studies on enzymatic lignin degradation rely on white-rot fungi, which can mineralise lignin to CO2 and H2O in pure cultures [65, 66]. Among these fungi are
In summary, microbial degradation of lignocellulosic material requires a concerted action of a variety of enzymes arranged in an enzymatic complex, depending on the biomass to be degraded. The gene expression, production and secretion of plant cell wall-degrading enzymes demand energy from the microbial cells and therefore the overall process is highly regulated. There is an intense cross-talk in induction of expression of the genes encoding different classes of enzymes. The control of the regulation of CWDEs production could be the key for the development of new microbial strains that efficiently produce and secrete CWDEs. The regulation of genes encoding polysaccharide-degrading enzymes will be the subject of the next section of this chapter.
10. Regulation of cell-wall degrading enzymes production in fungi
The production of CWDEs by fungi is an energy-consuming process. The fine-tuned regulation of genes encoding CWDEs ensures that these enzymes will be produced only under conditions in which the fungus requires plant polymers as carbon source. Readily metabolizable carbohydrates repress the synthesis of enzymes related to catabolism of alternative carbon sources such as plant cell wall polysaccharides. In this way, preferential utilization of the most favored carbon source prevails, and one of the regulatory mechanisms involved in this adaptation is carbon catabolite repression (CCR). The CCR is activated by many carbon sources, depending on the lifestyle of the microorganism, but usually glucose is the most repressive molecule . Nowadays, the search for microorganisms able to efficiently degrade lignocellulosic biomass is pivotal for the establishment of sustainable production of biomass-derived ethanol and other biocompounds. In this context, CCR appears as a major challenge to overcome, once this mechanism is responsible for enzymatic exclusion of less preferred carbon source such as lignocellulose-derived sugars. Hence, the comprehension of molecular mechanisms behind CCR, as well as the transcriptional control of cell wall derived enzymes are prerequisite in order to develop new microbial strains for lignocellulose degradation. In this section, the induction of expression of cellulases and hemicellulases, the transcriptional control of genes encoding CWDEs and the overall mechanism behind CCR will be discussed.
11. Induction of cellulases
Although the biochemistry of the process behind lignocellulosic degradation has been studied in detail, the mechanism by which filamentous fungi sense the substrate and initiate the overall process of hydrolases production is still unsolved. Some researchers have been proposed that a low constitutive level of cellulase expression is responsible for the formation of an inducer from cellulose, amplifying the signal. Another group of scientists suggest that the fungus initiates a starvation process, which could in turn activates cellulase/hemicellulase expression. Also, it is possible that an inducing sugar derived from carbohydrates released somehow from the fungal cell wall could be the derepressing molecules for hydrolase induction. Despite of the fact that the true mechanism behind natural cellulase/hemicellulase induction is still lacking, some individual molecules are known to induce these hydrolases.
Cellobiose (two β-1,4-linked glucose units) appears to induce cellulase expression in many species of fungi. Cellobiose is formed as the end product of cellobiohydrolases activity, and it has been show to induce cellulase expression in
Moreover, induction of cellulase genes could be achieved in
12. Induction of hemicellulases and pectinases
Hemicellulase expression has been studied mostly in Aspergilli and
The monosaccharide D-xylose is a well-known inducer of xylanolytic enzymes in
The genes encoding enzymes responsible for the degradation of arabinoxylan in
Regarding to pectinolytic enzymes, D-galacturonic acid, polygalacturonate and sugar beet pectin have been shown to induce virtually all the genes encoding for pectin degradation enzymes in
Complex mixtures of polysaccharides have been shown to induce a wide range of cellulases/hemicellulases genes in
13. Induction of ligninases
The ligninolytic system of many fungi appears to be induced under nutrient deprivation, mainly nitrogen, carbon and sulphur. Therefore, the expression of most of the ligninolytic genes is regarded as a stress response to nutrient deprivation. Also, the presence of Mn(II) is required for induction of manganese peroxidase (MnPs) genes in the white-rot fungi
Laccases are multicopper oxidase proteins, and therefore can be induced by copper, although other metals can induce the expression of laccase genes as well, such as manganese and cadmium [105, 106]. Many natural and xenobiotic aromatic compounds, which are often related to lignin or humic substances, were shown to induce genes related to laccases . In general, it has been postulated that laccases are the first enzymes degrading lignin, and possible further degradation products released from the polymer could act as inducers to amplify laccase expression, and subsequently induce other ligninolytic genes .
14. Transcription factors involved in the expression of cellulase and hemicellulase-encoding genes
A number of genes encoding plant cell wall degrading enzymes appears to present in their promoter regions regulatory elements for binding of transcriptional activators. The filamentous fungi
15. The transcriptional activator XlnR
Complementation by transformation of an
The XlnR transcriptional activator belongs to the class of zinc binuclear cluster domain proteins (PF00172) . The DNA-binding domain is found in the XlnR at the N-terminal of the protein and, in addition to this domain, a fungal specific transcription factor domain is also present (PF04082) . Functional studies have been demonstrated that a putative coiled-coil domain is important for the XlnR function, as the disruption of the α-helix structure (Leu650Pro mutation) lead to cytoplasmic localization and loss of function of XlnR, due to a loss of transcription of the structural genes of the regulon . As demonstrated by the same study, a C-terminal portion of XlnR appeared to be involved in transcriptional regulation, as a deletion of some amino acids of the C-terminus increased the expression of XlnR target genes, even under D-glucose repression conditions . Efforts have been done in order to evaluate the behavior of XlnR regulon to optimize the expression of target genes. For instance, a modeling study for the observation of XlnR regulon dynamics under D-xylose induction was performed. In this study, it was demonstrated that regulation of the
16. The transcriptional regulators Xyr1, Ace1 and Ace2
Ace2 belongs to a zinc-binuclear cluster DNA-binding protein and appears to be an activator of cellulase and hemicellulase genes in cellulose-induced cultures of
17. Other regulators involved in plant polysaccharide degradation in Aspergilli
The enzymatic system responsible for plant polysaccharide degradation is induced and commonly amplified after releasing of the plant cell wall polymers components. Two important components of the plant cell wall are D-xylose and L-arabinose, present in the polymers arabinan, arabinogalactan, xyloglucan and xylan. In Aspergilli, D-xylose and L-arabinose are catabolized through the pentose catabolic pathway, PCP , consisting of a series of reversible reductase/dehydrogenase steps culminating with the formation of D-xylulose-5-phosphate, which enters the pentose phosphate pathway (PPP). In
Furthermore, it was found that in
AmyR is another transcriptional activator found in Aspergilli. AmyR was first described as a transcriptional regulator of genes encoding enzymes involved in starch and maltose hydrolysis . Nowadays, studies have been demonstrated a broader role for AmyR, which appears to regulate another gene expression systems. High levels of both α- and β-glucosidase as well as α- and β-galactosidase in the
18. Transcriptional regulators of plant polysaccharide degradation genes in Neurospora crassa
The filamentous ascomycete fungus
In fact, studies assessing a near-full genome deletion strain set in
19. Carbon catabolite repression in Aspergilli
As briefly described above, microorganisms are known to adjust their carbon metabolism in order to minimize energy demands. One of these regulatory mechanisms is the carbon catabolite repression (CCR). Readily metabolizable carbon sources, such as glucose, are preferably catabolized and, in general, suppress the utilization of alternative carbon sources, repressing mainly the enzymatic system required for the catabolism of less favorable carbohydrates. For general carbon catabolite repression in some Aspergilli species, the DNA-binding Cys2His2 zinc-finger repressor CreA is absolutely necessary . In general, the negative effect of this regulatory system depends on the concentration of the preferable carbon source (elicitor). For instance, higher concentrations of the elicitor usually induce stronger transcriptional repression . The presence of the repressing elicitors initiates signal transduction pathways to result in transcriptional repression of the catabolism of poor carbon sources. In this context, the molecular mechanisms leading to CCR is well known for the ethanol utilization in
In this context, CreA appears as a sole transcriptional repressor of the system, exerting its function in the presence of a co-repressor [139, 142 - 143]. It is well known that in the
A variety of studies have been demonstrated the mechanisms through which CreA represses some polysaccharide-degrading enzymatic systems in fungi. It was shown that CreA appears to repress
F-box proteins are proteins containing at least one F-box domain in their structures. The F-box domain is a protein structural motif of about 50 amino acids that mediates protein-protein interactions . Usually, F-box proteins mediate ubiquitination of proteins targeted for degradation by the proteasome, but these proteins have also been associated with cellular functions such as signal transduction and regulation of cell-cycle . A study that performed a screening of 42
In summary, an intricate and fine-tuned regulation network exists in order to control the expression of plant cell-wall degradation genes in fungi. A variety of transcriptional regulators are able to respond to different nutritional requirements of the fungus, depending on its lifestyle. In general, readily metabolizable carbon sources such as glucose represses the transcription of genes responsible for the poor carbon source catabolism, via different mechanisms. The carbon catabolite repression in fungi is a common mechanism of regulation through which the organism adapts to nutritional availability in their environment. For instance, in
20. Improving microbial strains for degradation of lignocellulosic biomass
In order to degrade efficiently plant biomass, a microorganism should possess characteristics that make the process economically viable. For cellulosic ethanol production, for instance, an efficient microorganism should produce high yields of the desired product, must have a broad substrate range and high ethanol tolerance and it has to be tolerant to the inhibitors present in lignocellulosic hydrolysates. Therefore, engineering microbial strains for improvement of effectiveness in industrial applications is not a simple task. Concerning to bioethanol production, the most promising organism for genetic bioengineering is the yeast
However, the metabolism of
While most biological routes being studied for the processing of lignocellulosic biomass focused on the separate production of hydrolytic enzymes, in a process that usually comprises several steps, another approach is suggested to achieve this goal. This approach, termed consolidated bioprocessing (CBP) involves the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars in a single stage via microorganisms or a consortium . CBP appears to offer very large costs reduction if microorganisms can be developed that possess the required combination of substrate utilization and product formation properties . In a 2006 report in biomass conversion to biofuels, the U.S. Department of Energy endorsed the view that CBP technology is "the ultimate low-cost configuration for cellulose hydrolysis and fermentation" (DOE Joint Task Force, 2006; energy.gov). Currently, CBP technology is developing fast, especially due to partnerships with venture capital investors and researchers. The main challenge of CBP is to generate engineered microorganisms able to produce the saccharolytic enzymes and converting the sugars released by those enzymes into the desired end-products. In addition, CBP microorganisms need to be able to perform these tasks rapidly and efficiently under challenging, industrial processes. A successful microbial platform for production of bioethanol from microalgae is currently available, and demonstrates an application of the CBP . A DNA fragment encoding enzymes for alginate transport and metabolism from
The approach required for generation of CBP microorganisms involves the knowledge of many topics discussed in this chapter, concerning to fundamental principles of microbial cellulose utilization and its regulation. Moreover, the principles of synthetic bioengineering discussed above can be applied to the development of new strains for CBP technology, and therefore the generation of new microbial platforms able to uptake and metabolize completely the lignocellulosic biomass.
21. Conclusions and future perspectives
A large quantity of lignocellulosic residues is accumulating over the world, mainly due to the expansion of industrial processes, but other sources such as wood, grass, agricultural, forestry and urban solid wastes contribute to accumulation of lignocellulosic material. These residues constitute a renewable resource from which many useful biological and chemical products can be derived. The natural ability of fungi and other microorganisms to degrade lignocellulosic biomass, due to highly efficient enzymatic systems, is very attractive for the development of new strategies concerning industrial processes. Paper manufacture, composting, human and animal feeding, economically important chemical compounds and biomass fuel production are among some industrial applications derived from microbial lignocellulosic degradation.
Global climate change and future energy demands initiate a race in order to achieve sustainable fuels derived from biomass residues. Conversion of sugars to ethanol is already currently done at very low cost from sugarcane in Brazil, and from corn, in United States. However, the challenge is how to obtain the biofuel from the wastes generated from the mills producing ethanol. Residues such as sugarcane bagasse and corncobs contain large amounts of lignocellulosic material and therefore can be transformed into biofuels. A major advantage of using residues to produce biofuels is to reduce the competition between fuels and food. In this context, hydrolytic enzymes such as cellulases contribute for the large cost of cellulosic ethanol nowadays. The great bottleneck to achieve cellulosic biofuels is the plant biomass recalcitrance, and overcome such barrier is the key for the development of feasible industrial processes for biofuels production. For instance, it was recently demonstrated that
The comprehension of the machinery behind the enzymatic systems of fungi able to degrade plant cell wall polysaccharides favors the use of the microorganisms in industrial applications. Currently, through advanced molecular techniques, it is possible to engineer new microbial strains by insertion or deletion of genes involved in important metabolic pathways responsible for biomass degradation. The useful host cells to develop the synthetic bioengineering should have versatile genetic tools, resources and suitability for bio-refinery processes, such as stress tolerance. Therefore, a strain development in future requires insertion, deletion and expression controls of multiple genes and it is a difficult task to achieve. However, integrated advanced techniques could be able to overcome these challenges, including computational simulation of metabolic pathways, genome synthesis, directed evolution and minimum genome factory. The synthesis of the whole genome has already been done [160, 162] and, as discussed in reference , in a near future the synthesis of very large fragments of DNA will make it possible to design a whole yeast artificial chromosome (YAC) encoding a number of genes. According to these authors, the
As said by Lee Lynd, a pioneering researcher in the field of biomass: "the first step toward realizing currently improbable futures is to show that they are possible". These technologies described above are currently available for scientific community and, along with advances in industrial processes, endorse the possibility to take energy from plant biomass using microorganisms. Thus, the Humanity has never been so close to use new and sustainable ways of energy.
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