smg67-+Draft

=An Introduction to the Current Literature on Cellulose, Cellulase and the Hydrolytic Enzymatic Reaction of Cellulase on Cellulose=

Abstract
Cellulolytic organisms have an important role on earth by degrading cellulose, the most plentiful compound on the planet. Cellulose has a simple polymer structure, but it forms insoluble crystalline microfibrils macrostructure which is resistant to enzymatic hydrolysis. All known organisms that degrade cellulose produce a group of "synergistic" enzymes with different functions that act together. Cellulase research on the molecular level has elucidated some of the structures and mechanisms that contribute to their activity. Despite the considerable variety, comparisons show that the catalytic cores of cellulases belong to a small number of families. Within each family, the current data show that the variety of enzymes share: a common folding pattern, the same catalytic residues, and the same reaction mechanisms, (either single substitution with inversion of configuration or double substitution with retention of the β-configuration at the anomeric carbon). In addition to the catalytic domains, many cellulolytic enzymes (cellulases, xylanases etc.) contain domains not directly concerned with catalysis, but which assist in substrate binding, multi-enzyme subunit complexation, or attachment to the cell surface. It is assumed these domains assist in the catalysis of crystalline cellulose by: not allowing the enzymes to be washed from the surface of the substrate, by focusing catalysis on certain areas in which the substrate is weakened by multiple hydrolytic events. In most cellulolytic organisms, cellulase synthesis is inhibited in the presence of easily hydrolyzed, soluble carbon sources (usually the product of hydrolysis) and promoted in the presence of cellulose (substrate). Several applications of cellulases and hemicellulases exist for textile, food, and paper pulp processing. These applications rely on the modification of cellulose and hemicellulose by partial hydrolysis. Total hydrolysis of cellulose into glucose is not yet economically feasible. However, the desire to reduce greenhouse emissions and petroleum dependance provides an added incentive for the development of processes generating fuels from cellulose, a major renewable carbon source.

I. Introduction
The prospect of producing fuel from cellulosic biomass, the largest carbon source on earth, has resulted in large investments in the biofuel industry in the recent past (Schubert, 2006; Sheridan, 2008; Waltz, 2007). Cellulosic ethanol is produced via four major consecutive steps: pretreatment, hydrolysis, fermentation, and separation. Currently improvements are necessary in the enzymatic hydrolysis of cellulosic biomass in order to economically realize cellulosic ethanol. Compared to corn ethanol and petroleum derived gasoline cellulosic ethanol is rather uneconomical (Galbe and Zacchi, 2002; Lynd et al., 2008; Sun and Cheng, 2002). The current challenges include poor rate of hydrolysis, cost of cellulases, and lack of information about the cellulase cellulose “system” and its governing properties. The benefits of cellulosic ethanol over current hydrolysis methods, such as acid hydrolysis, include less expense (cooling water, gas, and electricity), decreased disposal cost and no corrosion issues (Sun and Cheng, 2002). Cost reduction is the main driving factor behind the current surge of interest in cellulosic fuels and subsequent cellulose-cellulase interest (Lynd et al., 2008). Better technologies can be created by improving upon the current cellulases as well as by improving the cellulosic substrates (Himmel et al., 2007). To do so it is necessary to understand the enzyme-substrate interactions and identify the contribution of various properties of the substrate, enzyme, and environment to the hydrolysis process. This paper will discuss in depth the chemical structure and biological morphology of several types of celluloses and cellulases with an emphasis on research presented up to the present.

II. Cellulose
Cellulose forms the chief element of green plants and wood. It is the most abundantly available natural material and nature produces between 10^10 and 10^11 tons of cellulose each year. Cellulose is a linear polysaccharide of repeating d-glucopyranose units linked by β-(1,4) linkages. The degree of polymerization of cellulose depends largely on the plant species but is approximately 10,000 for wood and 15,000 for cotton. Natural cellulose is a semicrystalline polymer with crystalline sections produced by polymer alignment and held together by strong hydrogen bonding (in-plane) and Van der Waals interactions (between planes). There are four different allomorphs (similar forms) for cellulose: cellulose I (Iα and Iβ), cellulose II, cellulose III (IIIi and IIIii) and cellulose IV (IVi and IVii), and they can easily be transformed from one form to another by chemical treatment (O’Sullivan, 1997). While cellulose III is thermodynamically the most stable form, it is cellulose I which is most commonly found in nature. The Iα allomorph is predominant in primitive organisms, while Iβ is the predominant allomorph in plants. Iβ can also be obtained from Iα by water treatment at 260–280 ◦C for 15–30 min (Debzi et al., 1991). Often found in cell-walls alongside cellulose is hemicellulose, which is a term first coined by Schulze (Schulze 1891). This group of polysaccharides is obtained by extracting materials containing cell-walls with alkali. Hemicelluloses have a random amorphous structure and are comprised of several polysaccharides (Muralikrishna and Rao, 2007). Starch is a naturally occurring blend of two polymers: amylase and amylopectin. Both are α-d-glucopyranose polymers. For standard starches, the amylose to amylopectin ratio varies from 1:4 to 1:2 (Tester and Karkalas, 2004). “Amylose-rich” and “waxy” starch varieties have greater amounts of amylose and amylopectin, respectively. Amylose is a linear homopolysaccharide formed with d-glucopyranose units linked together with α-(1,4) linkages. The average degree of polymerization (DP) of amylose is between 300 and 25,000. Amylopectin is a branched homopolysaccharide formed with d-glucopyranose units. The rate of branching is about every 20 units. In each chain, units are linked by α-(1,4) linkages and the side-chains are linked to the main chain by α-(1,6) linkages. The number of glucose units is between 105 and 109, depending on the origin of the starch. Starch a is a semicrystalline polymer found in three different allomorphs: the A allomorph is found in cereals, the B allomorph is found in tubers, while the C allomorph is found in legumes, roots, fruits and is actually a combination of both A and B allomorphs (Veregin, Fyfe, and Marchessault, 1986; Buleon, Gerard, and Chanzy, 1998). The crystalline sections are formed by alignment of the sidechains of amylopectin alongside the backbone. Both the amount and length of branching of the amylopectin affects the crystalline nature.

Lignin is the second most abundant, naturally occurring macromolecule. It is found as cell-wall component in all "vascular plants" and coexists with cellulose (Nimz, 2000). Since lignin is largely hydrophobic and cellulose is hydrophilic, they are made compatible by the presence of hemicelluloses, which have both hydrophilic and hydrophobic regions. Lignin acts as permanent glue, binding cells together in the woody stems, and gives the stems their rigidity and impact resistance. Payen discovered lignin in 1838 during the treatment of wood with nitric acid and alkaline solutions (Payen, 1838). These treatments produced an insoluble fraction designated cellulose, and a soluble fraction which he called "incrustant." This soluble material was later named “lignin” by Schulze (Schulze, 1891). Lignin is generally defined as polymeric natural products derived from an enzyme catalyzed “dehydrogenative polymerization” of three precursors: trans-coniferyl, trans-sinapyl and trans-ρ-coumaryl alcohol (Nimz, 2000). Lignin is the name for lignin extracted from wood, while lignin still part of the plant tissue is considered "proto-lignin". The enzyme catalyzed (initiated) polymerization results in bonds of outstanding stability. The only weak bond which is only relatively weak and able to be hydrolyzed is the α-aryl ether bond. These stable bonds make lignin very difficult to degrade and only under harsh conditions can the more stable ether bonds be hydrolyzed. The plant type determines the final structure of lignin. Due to the similarity in the base structure of the lignin precursors, each molecule of lignin contains a series of phenyl–propane units. Lignins are categorized into two major groups: guaiacyl and guaiacyl–syringyl lignins (Nimz, 2000). The guaiacyl lignins category is populated mostly by gymnosperm lignins, while the guaiacyl–syringyl lignin category contains the angiosperm and herbaceous lignins. These categories are not definite as different lignins can coexist, even in the same plant. Guaiacyl lignins contain p-hydroxyphenyl propane (no methoxy group on the aromatic ring) and guaiacyl propane units (one methoxy group on the aromatic ring ). The guaiacyl-syringyl lignins contain syringyl propane units (two methoxy groups on the aromatic ringl) (Nimz, 2000).

II. Cellulase
Cellulases, glycosyl hydrolase enzymes, hydrolyze oligosaccharides and polysaccharides (Henrissat, 1991; Henrissat et al., 1989, 1998). Cellulases are modular in nature; each module consists of a successive portion of the polypeptide chain and forms a distinct unit. While there are modular variations, all cellulases possess a catalytic domain, which is a glycosyl hydrolase according to its amino acid sequence .Within a given family, the positions of the catalytic residues are conserved. The three-dimensional structures of cellulases and related enzymes from 15 different families, which coincide with 5 different protein folds, are currently known (Davies and Henrissat, 1995; Henrissat and Davies, 1997; White and Rose, 1997).

The cellulosomal (the cellulosome is a complex consisting of multiple cellulases and related enzyme subunits) enzyme subunits are not different from the free cellulases. Both free cellulases and cellulosomal enzymes contain similar types of catalytic domains all from one family of glycosyl hydrolase. The important difference between the two types of enzymes is that all cellulosomal enzymes currently known contain a dockerin domain, which attaches it to the cellulosome, whereas noncellulosomal enzymes do not contain this dockerin domain (Bayer et al., 1994; Beguin and Lemaire, 1996). In bacteria, the dockerin domain measures approximately seventy amino acids long, of which twenty two residues repeat (Tokatlidis et al., 1991).

In place of a dockerin domain, noncellulosomal cellulases usually contain at least one copy of a cellulose-binding module (CBM). The CBM serves to direct a given catalytic domain to the substrate (Tomme et al., 1995). Several cellulosomal enzymes also contain CBMs, however the presence of a CBM seems not to be a definitive character of cellulosomal cellulases, and its role is not always that of a targeting mediator. For this task, the cellulosomal enzymes collectively rely on a special CBM, carried by a scaffolding subunit.

C. thermocellum has become the model organism for cellulase research due to the numerous studies on it to date. Its cellulase system displays an exceptional wealth, diversity, and intricacy of enzymatic components, making C. thermocellum the foremost cellulose-degrading organism currently known. The cellulosomal enzymes from C. thermocellum vary in size from 40kDa to 180 kDa. The smaller cellulases (70 kDa) are characterized by a single catalytic domain attached to a dockerin domain. As the cellulosomal enzymatic subunits become larger, they generally take on additional modules. One exemption is the comparatively large CelS, which appears to contain only a single catalytic domain together with its dockerin (Kruus et al., 1993). The native CelS catalytic domain, proteolytically clipped from its neighboring dockerin domain, was isolated from the cellulosome in viable form, and its properties were investigated (Lamed et al., 1991). CelS was described as the chief cellulosomal cellobiohydrolase, which shows a processive type of activity whereby a cellulose chain is cleaved sequentially. The native enzyme was shown to be inhibited by cellobiose (product of enzymatic hydrolysis), a typical property of the intact cellulosome

Carbohydrate Binding Modules (CBM)
Another cellulase of importance has a “Family-9” catalytic domain. The //C. thermocellum// cellulosome includes four such enzymes ( CelD, CelF, CbhA, and CelJ). Crystal structures, showing subtypes of these glycosyl hydrolases are currently known. The crystal structures give important information about the modular nature of cellulases. The structure of the Family-9 catalytic domain is very similar, displaying an (α/α)6-barrel fold and equivalent catalytic machinery. They tend to differ in their neighboring modules which "co-crystallized" with the catalytic domains. The catalytic domain of the cellulosomal CelD from //C. thermocellum// was the first cellulase to have been crystallized, also the structure showed an "N-terminal neighboring seven-stranded immunoglobulin like (Ig) domain" of unknown function (Juy et al., 1992). Another crystal structure is known for a different type of Family-9 catalytic domain from a thermophilic aerobe (//Thermomonospora fusca//). This cellulase (equivalent to CelF from the //C. thermocellum// cellulosome) lacks the Ig domain; however its catalytic domain (Family-9) is linked to a C-terminal, Family-III CBM (Sakon et al., 1997). In general CBMs are believed to act in the binding of the catalytic domain to the substrate. The CBM is connected to the catalytic domain via a chainlike linker domain. The CBM also acts to disrupt the substrate in order for the catalytic domain to more effectively bind it (Borasten et al.,2004).

The aforementioned CBM of //T. fusca// is unusual. Most of the cellulose-binding residues are not conserved, and the CBMs of this subtype have thus been classified as a subfamily (IIIc). Family-IIIc CBMs have been proposed to act with the catalytic domain by binding loosely to the incoming cellulose chain, which is then "fed" into the active-site for hydrolysis. This type of CBM is not involved in the initial binding to crystalline cellulose, but acts more so in the catalytic function by promoting processivity (Bayer et al., 1998,Gal et al., 1997; Irwin et al., 1998).

The information from the Family-9 enzymes suggests that the catalytic domains can be adapted by helper modules, which can alter the properties of an enzyme. Often in nature a given type of module is found nearby to a specific type of catalytic domain suggesting an important theme. Another theme among cellulolytic enzymes is the connection of an N-terminal Family-IV CBM with an Ig-associated Family-9 cellulase. The ways in which CBM are associated with certain catalytic domains suggest a particular function for the CBMs. The CBM's connection with certain types of catalytic domain could indicate a role whereby they bind a certain conformation of cellulose and feed the chain into the active-site of its nearby catalytic domain.

Multiple Substrate Enzymes
Many of the larger cellulosomal enzyme subunits in //C. thermocellum// possess more than one catalytic domain. Even some xylanases (enzymes closely related to cellulase) contain an additional enzymatic module that exhibits esterase activity. The two catalytic domains may act in concert on the hemicellulose of the plant cell wall; hydrolyzing the xylan chain while separating it from the lignin component. Similarly, other examples of paired catalytic domains indicate concerted action on cellulosic substrates. (Bayer et al. 1994)

Scaffoldin
The enzymatic subunits of the cellulosome are organized by a specialized scaffoldin subunit. The scaffoldin subunits are very large, modular polypeptides. Each contains: a single CBM (Family-IIIa), one or more conserved hydrophilic modules (called X modules) of unknown function, and multiple copies of cohesin domains. There are two known types of scaffoldins. The C. thermocellum scaffoldin carries an internal CBM and a C-terminal type-II dockerin domain, which anchors it to the cell surface. The other species have N-terminal CBMs and lack a type-II dockerin. The dockerin domains of the Catalytic domains bind with the cohesin of the scaffoldin protein to give the cellulosome structure. The structural organization of the cellulosomes in nature might show much greater diversity (Bayer et al. 1994).

Although the entire structure of the cellulosome is not entirely known, the guiding principles that seem to govern the organization of its various subunits into the cellulosomal complex seem to be resolved. The dockerin domains of the enzymatic subunits engage in a very stable type of binding interaction with the cohesin domains of the scaffoldin subunit. The binding is calcium dependent (Choi and Ljungdahl, 1996; Lytle et al., 1996; Yaron et al., 1995). There seems to be no specificity in the binding among the cohesins and the dockerins within a given cellulosome. The various cohesins seem to recognize nearly all of the dockerins equally. It would seems that the enzymatic subunits would be incorporated into the cellulosome in a random manner, which would generate heterogeneity in cellulosome composition. Evidence of this has been reported for, C. papyrosolvens (Pohlschroder et al., 1995). However the question of random or selective incorporation of the cellulosomal subunits into the complex is still an open issue.

III Hydrolysis
The hydrolysis reaction catalyzed by glycosidases (including cellulases and xylanases) proceeds via an acid-base mechanism involving two specific residues. The first residue acts as an acid catalyst and protonates the oxygen of the osidic bond. The other residue acts as a nucleophile, which either interacts with the oxocarbonium intermediate or promotes the formation of an (OH-) ion from a water molecule. The reaction proceeds via retention or inversion of configuration. Reactions leading to retention of configuration require a two-step mechanism, including a double inversion of configuration at the anomeric carbon, and the formation of an oxocarbonium intermediate (Sinnot, 1990). The model of this type of reaction is the mechanism of lysozyme (Kelly et al., 1979). Reactions leading to inversion of configuration occur via a nucleophilic substitution (Sinnot, 1990) ). Enzymes of family 5, 7, 10 and 11 proceed with retention of configuration. Enzymes of family 6 and 9 proceed with inversion of configuration. Proton donating residues have been identified in T. reesei CBH II (Asp-221) C. thermocellum endoglucanase CelD (Glu-555) (Juy et al., 1992), B. pumilus xylanase XynA (Glu-182) (Ko et al.,1992), Bacillus polymyxa and Bacillus subtills endoglucanases (Baird et al.,1990), Erwinia chrysanthemi endoglucanase CelZ (Py et al,1991), Clostridium cellulolyticum endoglucanase CelCCA and C. thermocellum endoglucanase CelC (Glu-140). Nucleophilic residues have been identified on the basis of structural analysis and mutagenesis data in C. thermocellum CelD (Asp-201) (Juy et al., 1992) and B. pumilus xylanase XynA (Glu-93) (Ko et al.,1992).

IV Summary/Conclusion
Cellulose is an organic polysaccharide (C6H10O5)n made up of a linear chain of several hundred to thousands of β(1→4) linked D-glucose units and is the structural component of the cell wall of green plants. Cellulose is the most abundant organic compound on Earth. It is insoluble in water and most organic solvents. It can be broken down by naturally occurring enzymes and chemically into its glucose units by acid treatment at high temperature. Cellulose molecules adopt an extended and stiff rod-like conformation, aided by the equatorial conformation of the glucose residues. The multiple hydroxyl groups on the glucose from one chain form hydrogen bonds with oxygen molecules on the same or on a neighbor chain, holding the chains firmly together side-by-side and forming microfibrils with high tensile strength. Cellulose is also very crystalline. Several different crystalline structures of cellulose are known, corresponding to the location of hydrogen bonds between and within strands. Many properties of cellulose depend on its chain length or degree of polymerization, the number of glucose units that make up one polymer molecule. Plant-derived cellulose is usually found in a mixture with hemicellulose, lignin, pectin and other substances, while microbial cellulose is quite pure, has a much higher water content, and consists of long chains.

Cellulosomes are produced by anaerobic microbes and deconstruct plant cell wall polysaccharides. Molecular integration of cellulases and hemicellulases into cellulosomal multienzyme complexes results from the high-affinity interaction established between type I dockerin domains of the modular enzymes and type I cohesin modules of a noncatalytic scaffoldin. Cellulosomes bind the plant cell wall primarily through a scaffoldin-borne carbohydrate binding module (CBM). In addition, cellulosomes may be anchored to the microbial cell surface through the interaction of a type II dockerin located in the scaffoldin and type II cohesin domains located at the cell envelope. Integration of the microbial biocatalysts into cellulosomes potentiates catalysis through the maximization of enzyme synergism afforded by enzyme proximity and efficient substrate targeting. Cellulosomal dockerins display a dual cohesin-binding interface that may introduce enhanced flexibility in the quaternary organization of the multienzyme complex.

The hydrolysis reaction proceeds via an acid-base mechanism involving two specific residues. The reaction proceeds via retention or inversion of configuration. Reactions leading to retention of configuration require a two-step mechanism, including a double inversion of configuration at the anomeric carbon, and the formation of an oxocarbonium intermediate. Reactions leading to inversion of configuration occur via a nucleophilic substitution.

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