From Soil to Structure,a Novel Dimeric β-Glucosidase Belonging to Glycoside Hydrolase Family 3 Isolated from Compost Using Metagenomic Analysis

A recent metagenomic analysis sequenced a switchgrass-adapted compost community to identify enzymes from microorganisms that were specifically adapted to switchgrass under thermophilic conditions. These enzymes are being examined as part of the pretreatment process for the production of “second-generation” biofuels. Among the enzymes discovered was JMB19063, a novel three-domain β-glucosidase that belongs to the GH3 (glycoside hydrolase 3) family. Here, we report the structure of JMB19063 in complex with glucose and the catalytic variant D261N crystallized in the presence of cellopentaose. JMB19063 is first structure of a dimeric member of the GH3 family, and we demonstrate that dimerization is required for catalytic activity. Arg-587 and Phe-598 from the C-terminal domain of the opposing monomer are shown to interact with bound ligands in the D261N structure. Enzyme assays confirmed that these residues are absolutely essential for full catalytic activity.     

Exploration of New Geometries in Cellulosome-Like Chimeras

In this study, novel cellulosome chimeras exhibiting atypical geometries and binding modes, wherein the targeting and proximity functions were directly incorporated as integral parts of the enzyme components, were designed. Two pivotal cellulosomal enzymes (family 48 and 9 cellulases) were thus appended with an efficient cellulose-binding module (CBM) and an optional cohesin and/or dockerin. Compared to the parental enzymes, the chimeric cellulases exhibited improved activity on crystalline cellulose as opposed to their reduced activity on amorphous cellulose. Nevertheless, the various complexes assembled using these engineered enzymes were somewhat less active on crystalline cellulose than the conventional designer cellulosomes containing the parental enzymes. The diminished activity appeared to reflect the number of protein-protein interactions within a given complex, which presumably impeded the mobility of their catalytic modules. The presence of numerous CBMs in a given complex, however, also reduced their performance. Furthermore, a “covalent cellulosome” that combines in a single polypeptide chain a CBM, together with family 48 and family 9 catalytic modules, also exhibited reduced activity. This study also revealed that the cohesin-dockerin interaction may be reversible under specific conditions. Taken together, the data demonstrate that cellulosome components can be used to generate higher-order functional composites and suggest that enzyme mobility is a critical parameter for cellulosome efficiency.     

Genetic diversity detection and gene discovery of novel glycoside hydrolase family 48 from soil environmental genomic DNA

Sequence diversity within a family of functional enzymes provides a platform for novel gene development and protein engineering to improve the properties of these enzymes for further applications. Glycoside hydrolase family 48 (GH48) is an important group of microbial cellulases. However, the genetic diversity and gene discovery of GH48 enzyme in natural environments are rarely reported. In this study, the genetic diversity of GH48 from Changbai Mountain soil was evaluated by building a clone library via a culture-independent molecular method for the first time. Results showed that the genetic diversity of GH48 in Changbai Mountain soil was different from that in thermophilic compost and marine sediment libraries, and more than 80% of the sequences exhibited the highest identity with cellulase genes from Chloroflexi. Novel GH48 genes were also cloned, and the recombinants Cel48_hm01 and Cel48_hm02 were prokaryotically expressed, purified, and characterized. Characterization results suggested that they were probably endocellulases that adopted a catalytic mechanism similar to the GH48 cellulase from Clostridium. This study revealed the genetic distribution of glycoside hydrolases in soil environment, described Changbai Mountain soil as a valuable source for glycoside hydrolase gene screening, and presented supplementary property data on novel GH48 from natural soil environments.     

Structure-Function Relationships of Glucansucrase and Fructansucrase Enzymes from Lactic Acid Bacteria

Lactic acid bacteria (LAB) employ sucrase-type enzymes to convert sucrose into homopolysaccharides consisting of either glucosyl units (glucans) or fructosyl units (fructans). The enzymes involved are labeled glucansucrases (GS) and fructansucrases (FS), respectively. The available molecular, biochemical, and structural information on sucrase genes and enzymes from various LAB and their fructan and α-glucan products is reviewed. The GSand FS enzymes are both glycoside hydrolase enzymes that act on the same substrate (sucrose) and catalyze (retaining) transglycosylation reactions that result in polysaccharide formation, but they possess completely different protein structures. GS enzymes (family GH70) are large multidomain proteins that occur exclusively in LAB. Their catalytic domain displays clear secondary-structure similarity with α-amylase enzymes (family GH13), with a predicted permuted (β/α)₈ barrel structure for which detailed structural and mechanistic information is available. Emphasis now is on identification of residues and regions important for GS enzyme activity and product specificity (synthesis of α-glucans differing in glycosidic linkage type, degree and type of branching, glucan molecular mass, and solubility). FS enzymes (family GH68) occur in both gram-negative and gram-positive bacteria and synthesize β-fructan polymers with either β-(2→6) (inulin) or β-(2→1) (levan) glycosidic bonds. Recently, the first high-resolution three-dimensional structures have become available for FS (levansucrase) proteins, revealing a rare five-bladed β-propeller structure with a deep, negatively charged central pocket. Although these structures have provided detailed mechanistic insights, the structural features in FS enzymes dictating the synthesis of either β-(2→6) or β-(2→1) linkages, degree and type of branching, and fructan molecular mass remain to be identified.     

Synaptic Vesicle Exocytosis

Presynaptic nerve terminals release neurotransmitters by synaptic vesicle exocytosis. Membrane fusion mediating synaptic exocytosis and other intracellular membrane traffic is affected by a universal machinery that includes SNARE (for “soluble NSF-attachment protein receptor”) and SM (for “Sec1/Munc18-like”) proteins. During fusion, vesicular and target SNARE proteins assemble into an α-helical trans-SNARE complex that forces the two membranes tightly together, and SM proteins likely wrap around assembling trans-SNARE complexes to catalyze membrane fusion. After fusion, SNARE complexes are dissociated by the ATPase NSF (for “N-ethylmaleimide sensitive factor”). Fusion-competent conformations of SNARE proteins are maintained by chaperone complexes composed of CSPα, Hsc70, and SGT, and by nonenzymatically acting synuclein chaperones; dysfunction of these chaperones results in neurodegeneration. The synaptic membrane-fusion machinery is controlled by synaptotagmin, and additionally regulated by a presynaptic protein matrix (the “active zone”) that includes Munc13 and RIM proteins as central components.Synaptic vesicles are uniform organelles of ∼40 nm diameter that constitute the central organelle for neurotransmitter release. Each presynaptic nerve terminal contains hundreds of synaptic vesicles that are filled with neurotransmitters. When an action potential depolarizes the presynaptic plasma membrane, Ca²⁺-channels open, and Ca²⁺ flows into the nerve terminal to trigger the exocytosis of synaptic vesicles, thereby releasing their neurotransmitters into the synaptic cleft (Fig. 1). Ca²⁺ triggers exocytosis by binding to synaptotagmin; after exocytosis, vesicles are re-endocytosed, recycled, and refilled with neurotransmitters. Recycling can occur by multiple parallel pathways, either by fast recycling via local reuse of vesicles (“kiss-and-run” and “kiss-and-stay”), or by slower recycling via an endosomal intermediate (Fig. 1).Open in a separate windowFigure 1.The synaptic vesicle cycle. A presynaptic nerve terminal is depicted schematically as it contacts a postsynaptic neuron. The synaptic vesicle cycle consists of exocytosis (red arrows) followed by endocytosis and recycling (yellow arrows). Synaptic vesicles (green circles) are filled with neurotransmitters (NT; red dots) by active transport (neurotransmitter uptake) fueled by an electrochemical gradient established by a proton pump that acidifies the vesicle interior (vesicle acidification; green background). In preparation to synaptic exocytosis, synaptic vesicles are docked at the active zone, and primed by an ATP-dependent process that renders the vesicles competent to respond to a Ca²⁺-signal. When an action potential depolarizes the presynaptic membrane, Ca²⁺-channels open, causing a local increase in intracellular Ca²⁺ at the active zone that triggers completion of the fusion reaction. Released neurotransmitters then bind to receptors associated with the postsynaptic density (PSD). After fusion pore opening, synaptic vesicles probably recycle via three alternative pathways: local refilling with neurotransmitters without undocking (“kiss-and-stay”), local recycling with undocking (“kiss-and-run”), and full recycling of vesicles with passage through an endosomal intermediate. (Adapted from Südhof 2004.)Due to their small size, synaptic vesicles contain a limited complement of proteins that have been described in detail (Südhof 2004; Takamori et al. 2006). Although the functions of several vesicle components remain to be identified, most vesicle components participate in one of three processes: neurotransmitter uptake and storage, vesicle exocytosis, and vesicle endocytosis and recycling. In addition, it is likely that at least some vesicle proteins are involved in the biogenesis of synaptic vesicles and the maintenance of their exquisite uniformity and stability, but little is known about how vesicles are made, and what determines their size.     

Paleo-Immunology: Evidence Consistent with Insertion of a Primordial Herpes Virus-Like Element in the Origins of Acquired Immunity

Background

The RAG encoded proteins, RAG-1 and RAG-2 regulate site-specific recombination events in somatic immune B- and T-lymphocytes to generate the acquired immune repertoire. Catalytic activities of the RAG proteins are related to the recombinase functions of a pre-existing mobile DNA element in the DDE recombinase/RNAse H family, sometimes termed the “RAG transposon”.

Methodology/Principal Findings

Novel to this work is the suggestion that the DDE recombinase responsible for the origins of acquired immunity was encoded by a primordial herpes virus, rather than a “RAG transposon.” A subsequent “arms race” between immunity to herpes infection and the immune system obscured primary amino acid similarities between herpes and immune system proteins but preserved regulatory, structural and functional similarities between the respective recombinase proteins. In support of this hypothesis, evidence is reviewed from previous published data that a modern herpes virus protein family with properties of a viral recombinase is co-regulated with both RAG-1 and RAG-2 by closely linked cis-acting co-regulatory sequences. Structural and functional similarity is also reviewed between the putative herpes recombinase and both DDE site of the RAG-1 protein and another DDE/RNAse H family nuclease, the Argonaute protein component of RISC (RNA induced silencing complex).

Conclusions/Significance

A “co-regulatory” model of the origins of V(D)J recombination and the acquired immune system can account for the observed linked genomic structure of RAG-1 and RAG-2 in non-vertebrate organisms such as the sea urchin that lack an acquired immune system and V(D)J recombination. Initially the regulated expression of a viral recombinase in immune cells may have been positively selected by its ability to stimulate innate immunity to herpes virus infection rather than V(D)J recombination Unlike the “RAG-transposon” hypothesis, the proposed model can be readily tested by comparative functional analysis of herpes virus replication and V(D)J recombination.     

Structure and Kinetic Investigation of Streptococcus pyogenes Family GH38 α-Mannosidase

Background

The enzymatic hydrolysis of α−mannosides is catalyzed by glycoside hydrolases (GH), termed α−mannosidases. These enzymes are found in different GH sequence–based families. Considerable research has probed the role of higher eukaryotic “GH38” α−mannosides that play a key role in the modification and diversification of hybrid N-glycans; processes with strong cellular links to cancer and autoimmune disease. The most extensively studied of these enzymes is the Drosophila GH38 α−mannosidase II, which has been shown to be a retaining α−mannosidase that targets both α−1,3 and α−1,6 mannosyl linkages, an activity that enables the enzyme to process GlcNAc(Man)₅(GlcNAc)₂ hybrid N-glycans to GlcNAc(Man)₃(GlcNAc)₂. Far less well understood is the observation that many bacterial species, predominantly but not exclusively pathogens and symbionts, also possess putative GH38 α−mannosidases whose activity and specificity is unknown.

Methodology/Principal Findings

Here we show that the Streptococcus pyogenes (M1 GAS SF370) GH38 enzyme (Spy1604; hereafter SpGH38) is an α−mannosidase with specificity for α−1,3 mannosidic linkages. The 3D X-ray structure of SpGH38, obtained in native form at 1.9 Å resolution and in complex with the inhibitor swainsonine (K _i 18 µM) at 2.6 Å, reveals a canonical GH38 five-domain structure in which the catalytic “–1” subsite shows high similarity with the Drosophila enzyme, including the catalytic Zn²⁺ ion. In contrast, the “leaving group” subsites of SpGH38 display considerable differences to the higher eukaryotic GH38s; features that contribute to their apparent specificity.

Conclusions/Significance

Although the in vivo function of this streptococcal GH38 α−mannosidase remains unknown, it is shown to be an α−mannosidase active on N-glycans. SpGH38 lies on an operon that also contains the GH84 hexosaminidase (Spy1600) and an additional putative glycosidase. The activity of SpGH38, together with its genomic context, strongly hints at a function in the degradation of host N- or possibly O-glycans. The absence of any classical signal peptide further suggests that SpGH38 may be intracellular, perhaps functioning in the subsequent degradation of extracellular host glycans following their initial digestion by secreted glycosidases.     

Rapid Identification of Sequences for Orphan Enzymes to Power Accurate Protein Annotation

The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the “back catalog” of enzymology – “orphan enzymes,” those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme “back catalog” is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology’s “back catalog” another powerful tool to drive accurate genome annotation.     

Structural and biochemical studies of GH family 12 cellulases: improved thermal stability,and ligand complexes

In this review we will describe how we have gathered structural and biochemical information from several homologous cellulases from one class of glycoside hydrolases (GH family 12), and used this information within the framework of a protein-engineering program for the design of new variants of these enzymes. These variants have been characterized to identify some of the positions and the types of mutations in the enzymes that are responsible for some of the biochemical differences in thermal stability and activity between the homologous enzymes. In this process we have solved the three-dimensional structure of four of these homologous GH 12 cellulases: Three fungal enzymes, Humicola grisea Cel12A, Hypocrea jecorina Cel12A and Hypocrea schweinitzii Cel12A, and one bacterial, Streptomyces sp. 11AG8 Cel12A. We have also determined the three-dimensional structures of the two most stable H. jecorina Cel12A variants. In addition, four ligand-complex structures of the wild-type H. grisea Cel12A enzyme have been solved and have made it possible to characterize some of the interactions between substrate and enzyme. The structural and biochemical studies of these related GH 12 enzymes, and their variants, have provided insight on how specific residues contribute to protein thermal stability and enzyme activity. This knowledge can serve as a structural toolbox for the design of Cel12A enzymes with specific properties and features suited to existing or new applications.     

“Round Up the Usual Suspects”: A Comment on Nonexistent Plant G Protein-Coupled Receptors

An evolutionary argument supports the conclusion that plants do not have G protein coupled receptors.In the classic 1942 movie Casablanca, Vichy Police Captain Louis Renault obfuscated the truth by commanding his lieutenants to “round up the usual suspects,” knowing well that the culprit with the gun stood in plain view. Something similar has happened in the plant G protein field. This Scientific Correspondence was written to shed light on the source of misunderstanding and to preempt further confusion. Plant heterotrimeric G proteins are self-activating and therefore do not need and do not utilize G protein-coupled receptors (GPCRs). This conclusion was reached previously from biochemical analyses of plant G proteins (Johnston et al., 2007a; Urano et al., 2012); here, we buttress this point of view using an evolutionary argument. Proteins suspected as plant GPCRs were “rounded up” because they have the predicted topology of animal GPCRs and/or have been misannotated as such; however, these proteins are highly conserved in organisms that lack heterotrimeric G proteins. Therefore, they have functions unrelated to G-coupled signaling. Instead, the culprit protein standing in plain view is a receptor GTPase-accelerating protein (GAP), a receptor GAP called AtRGS1 (for regulator of G signaling).     

Mechanisms of Action of Bcl-2 Family Proteins

The Bcl-2 family of proteins controls a critical step in commitment to apoptosis by regulating permeabilization of the mitochondrial outer membrane (MOM). The family is divided into three classes: multiregion proapoptotic proteins that directly permeabilize the MOM; BH3 proteins that directly or indirectly activate the pore-forming class members; and the antiapoptotic proteins that inhibit this process at several steps. Different experimental approaches have led to several models, each proposed to explain the interactions between Bcl-2 family proteins. The discovery that many of these interactions occur at or in membranes as well as in the cytoplasm, and are governed by the concentrations and relative binding affinities of the proteins, provides a new basis for rationalizing these models. Furthermore, these dynamic interactions cause conformational changes in the Bcl-2 proteins that modulate their apoptotic function, providing additional potential modes of regulation.Apoptosis was formally described and named in 1972 as a unique morphological response to many different kinds of cell stress that was distinct from necrosis. However, despite the novelty and utility of the concept, little experimental work was performed during the following 20 years because no tools existed to manipulate the process. In the early 1990s, two seminal observations changed the landscape. First, as the complete developmental sequence of the nematode Caenorhabditis elegans was painstakingly elucidated at the single-cell level, it was noted that a fixed, predictable number of “intermediate” cells were destined to die, and that this process was positively and negatively regulated by specific genes. Second, a novel gene called B-cell CLL/lymphoma 2 (Bcl-2; encoded by BCL2) that was discovered as a partner in a reciprocal chromosomal translocation in a human tumor turned out to function not as a classic oncogene by driving cell division, but rather by preventing apoptosis. When it was discovered that the mammalian BCL2 could substitute for CED-9, the C. elegans gene that inhibits cell death, the generality of the process was recognized, and the scientific literature exploded with now well over 10⁵ publications on apoptosis. However, it is ironic to note that after a further 20 years of intensive investigation, it is clear that the mechanism of action of Bcl-2 is quite distinct from Ced-9, which sequesters the activator of the caspase protease that is the ultimate effector of apoptosis. In contrast, Bcl-2 works primarily by binding to other related proteins that regulate permeabilization of the mitochondrial outer membrane (MOM).This review examines how apoptosis is regulated by the members of the (now very large) Bcl-2 family, composed of three groups related by structure and function (illustrated in Fig. 1): (1) the BH3 proteins that sense cellular stress and activate (either directly or indirectly); (2) the executioner proteins Bax or Bak that oligomerize in and permeabilize the MOM, thereby releasing components of the intermembrane space that activate the final, effector caspases of apoptosis; and (3) the antiapoptotic members like Bcl-2 that impede the overall process by inhibiting both the BH3 and the executioner proteins. To understand the consequence of the interactions among the three subgroups, several models have been proposed (“direct activation,” “displacement,” “embedded together,” and “unified” models; illustrated in Fig. 2) that are briefly described here before a more detailed discussion of the Bcl-2 families.Open in a separate windowFigure 1.Schematic overview of the Bcl-2 family of proteins. The family is divided into two subgroups containing proteins that either inhibit apoptosis or promote apoptosis. The proapoptotic proteins are further subdivided functionally into those that oligomerize and permeabilize the MOM, such as Bax and Bak, or those that promote apoptosis through either activating Bax or Bak or inhibiting the antiapoptotic proteins, such as tBid, Bim, Bad, and Noxa. Proteins are included in the Bcl-2 family based on sequence homology to the founding member, Bcl-2, in one of the four Bcl-2 homology (BH) regions. All the antiapoptotic proteins, as well as Bax, Bak, and Bid, have multiple BH regions, are evolutionarily related, and share a three-dimensional (3D) structural fold. The BH3 proteins contain only the BH3 region, are evolutionarily distant from the multiregion proteins, and are intrinsically unstructured. Most members of the Bcl-2 family proteins contain a membrane-binding region (MBR) on their carboxyl termini in the form of a tail anchor, mitochondrial-targeting sequence, or as a hydrophobic amino acid sequence that facilitates binding and localization of these proteins to the MOM or to the endoplasmic reticulum (ER) membrane.Open in a separate windowFigure 2.Schematics of the core mechanisms proposed by various models for the regulation of MOMP by Bcl-2 proteins. (↑) Activation; (⊥) inhibition; (⊥↑) mutual recruitment/sequestration. Paired forward and reverse symbols indicate the model makes explicit reference to equilibria. (A) The direct activation model divides the different BH3 proteins by qualitative differences in function. The BH3 proteins with high affinity for binding and activating Bax and Bak are termed as “activators,” whereas those that only bind the antiapoptotic proteins are termed “sensitizers.” The activator BH3 proteins directly interact with and activate Bax and Bak to promote MOMP. The antiapoptotic proteins inhibit MOMP by specifically sequestering the BH3 activators. The BH3 sensitizer proteins can compete for binding with the antiapoptotic proteins, thus releasing the BH3 activator proteins to avidly promote MOMP through activation and oligomerization of Bax and Bak. (B) The displacement model categorizes the BH3 proteins solely based on their affinities of binding for the antiapoptotic proteins (hence, does not recognize them as activators). In this model, Bax and Bak are constitutively active and oligomerize and induce MOMP unless held in check by the antiapoptotic proteins. Therefore, for a cell to undergo apoptosis, the correct combination of BH3 proteins must compete for binding for the different antiapoptotic proteins to liberate Bax and Bak and for MOMP to ensue. (C) The embedded together model introduces an active role for the membrane and combines the major aspects of the previous models. The interactions between members of the Bcl-2 family are governed by equlibria and therefore are contingent on the relative protein concentrations as well as their binding affinities. The latter are determined by posttranslational modifications, fraction of protein bound to the membrane, and cellular physiology. At membranes, the activator BH3 proteins directly activate Bax and Bak, which then oligomerize, inducing MOMP. Both activator and sensitizer BH3 proteins can recruit and sequester antiapoptotic proteins in the membrane. The antiapoptotic proteins inhibit apoptosis by sequestering the BH3 proteins and Bax and Bak in the membrane or by preventing their binding to membranes. At different intracellular membranes, the local concentrations of specific subsets of Bcl-2 family members alter the binding of Bcl-2 proteins to the membrane and the binding equilibria between family members. As a result, Bcl-2 family proteins have distinct but overlapping functions at different cellular locations. (D) The unified model builds on the embedded together model by proposing that the antiapoptotic proteins sequester the activator BH3 proteins (mode 1) and sequester Bax and Bak (mode 2). It differs in that in the unified model, inhibition of apoptosis through mode 1 is less efficient (smaller arrow in panel D) and therefore easier to overcome by sensitizer BH3 proteins. In addition, the unified model extends the role of Bcl-2 family proteins and the regulation of MOMP to mitochondria dynamics (not shown).     

Effect of Linker Length and Dockerin Position on Conversion of a Thermobifida fusca Endoglucanase to the Cellulosomal Mode

We have been developing the cellulases of Thermobifida fusca as a model to explore the conversion from a free cellulase system to the cellulosomal mode. Three of the six T. fusca cellulases (endoglucanase Cel6A and exoglucanases Cel6B and Cel48A) have been converted in previous work by replacing their cellulose-binding modules (CBMs) with a dockerin, and the resultant recombinant “cellulosomized” enzymes were incorporated into chimeric scaffolding proteins that contained cohesin(s) together with a CBM. The activities of the resultant designer cellulosomes were compared with an equivalent mixture of wild-type enzymes. In the present work, a fourth T. fusca cellulase, Cel5A, was equipped with a dockerin and intervening linker segments of different lengths to assess their contribution to the overall activity of simple one- and two-enzyme designer cellulosome complexes. The results demonstrated that cellulose binding played a major role in the degradation of crystalline cellulosic substrates. The combination of the converted Cel5A endoglucanase with the converted Cel48A exoglucanase also exhibited a measurable proximity effect for the most recalcitrant cellulosic substrate (Avicel). The length of the linker between the catalytic module and the dockerin had little, if any, effect on the activity. However, positioning of the dockerin on the opposite (C-terminal) side of the enzyme, consistent with the usual position of dockerins on most cellulosomal enzymes, resulted in an enhanced synergistic response. These results promote the development of more complex multienzyme designer cellulosomes, which may eventually be applied for improved degradation of plant cell wall biomass.In nature, some anaerobic cellulolytic bacteria produce cellulosomes, which are organized by the action of scaffoldin subunits that usually contain a single carbohydrate-binding module (CBM) and multiple cohesin modules (2, 7, 13, 14, 28, 36). This arrangement allows the integration of several dockerin-containing enzymes into a complex, which is then targeted to the cellulosic substrate by the common CBM. The cellulosomal enzymes then exhibit enhanced synergistic activity, presumably due to their spatial proximity and coordinated interaction. In contrast, the enzyme systems of aerobic bacteria and fungi comprise free (uncomplexed) enzymes, which differ from cellulosomal systems in that many of them contain their own CBM that delivers the individual catalytic module to the surface of the substrate (39, 41, 42).In previous work, we used the designer cellulosome concept (5) to construct unique minicellulosomes of defined content (16, 32, 33). In order to construct designer cellulosomes, chimeric scaffoldins have been prepared which contained two or more cohesins that matched the dockerins of the enzymes (native cellulosomal or dockerin-fused chimeras). Enzymes that contain dockerins that match the specificity of a scaffoldin-borne cohesin can then be selectively integrated into the designer cellulosome at a specified site. Cellulosomal enzymes containing either a native dockerin or a divergent dockerin can be inserted on different sites of a chimeric scaffoldin. Alternatively, a free, noncellulosomal enzyme can be included in designer cellulosomes by replacing its native CBM with a dockerin of choice. In some cases, designer cellulosomes displayed enhanced synergistic activity over the parallel free-enzyme system (15, 17). This increased activity was shown to be a function of both a substrate-targeting effect (contributed by the CBM on the chimeric scaffoldin) and the enzyme proximity effect, thus supporting the initial hypothesis.In recent studies, we have investigated the free-cellulase system of Thermobifida fusca for use in designer cellulosome systems. This aerobic thermophilic cellulolytic bacterium contains a limited set of six free cellulases, each composed of a catalytic module and a crystalline-cellulose binding family 2 CBM (CBM2) module on either the N or C terminus of the protein. T. fusca contains three endoglucanases (Cel5A, Cel6A, and Cel9B), two exocellulases (Cel6B and Cel48A), and one processive endoglucanase (Cel9A). Previously, we converted both family 6 cellulases and the family 48 exoglucanase from the free to the cellulosomal mode of action by replacing their native CBM2s with a dockerin module (11, 12). All three chimeric enzymes exhibited cellulose-degrading activity on both soluble and crystalline substrates. The results indicated that the family 48 exoglucanase appeared to be well adapted to the cellulosomal mode of action, whereas the family 6 exoglucanase is less appropriate for inclusion into cellulosomes. Indeed, family 48 cellulases have been found to be a major component in every native cellulosome thus far described, in contrast to the family 6 cellulases, which have been identified only in free-cellulase systems.An important feature of the free-acting fungal and bacterial cellulases is that they contain a linker segment, often rich in prolines and threonines, that connects the catalytic module to the CBM (37). The role of such flexible linkers is thought to ensure independent action of the adjacent functional modules, thus allowing progressive and efficient hydrolysis of cellulose by the catalytic modules (6, 9, 10, 20, 25-27, 34, 36, 38, 40). The present communication focuses on the effect of linker length and dockerin position (relative to the catalytic module) on enzymatic activity within a designer cellulosome. For this purpose we have employed the highly active family 5 endoglucanase Cel5A from T. fusca (21, 22, 29), which was converted to the cellulosomal mode by replacement of its CBM with a dockerin module. Chimeric dockerin derivatives were prepared on either the N or C terminus of the Cel5A catalytic module, separated by linker segments of different lengths. In most cases, binary designer cellulosomes, comprising the respective Cel5A chimera together with a Cel48A chimera, were shown to be more efficient on crystalline cellulosic substrates than the combination of the wild-type free enzymes.     

Phylogenetic Analysis of α-Galactosidases of the GH27 Family

Amino acid sequence analysis of -galactosidases and other proteins of glycoside hydrolase family 27 (GH27) allowed isolation of three major subfamilies, 27a–27c. Unique isomalto-dextranase of Arthrobacter globiformis clustered separately. Eukaryotic proteins formed five clusters on a phylogenetic tree of the family. Bacterial GH27 proteins, which are relatively few, did not form stable clusters. A monophyletic origin of the GH27 family was demonstrated with the use of related proteins of the GH36 family. The structure of the active center and evolution of -galactosidases are discussed.     

Characterization of a novel theme C glycoside hydrolase family 9 cellulase and its CBM-chimeric enzymes

In bacterial cellulase systems, glycoside hydrolase family 9 (GH9) cellulases are generally regarded as the major cellulose-degrading factors besides GH48 exoglucanase. In this study, umcel9A, which was cloned from uncultured microorganisms from compost, with the encoded protein being theme C GH9 cellulase, was heterologously expressed in Escherichia coli, and the biochemical properties of the purified enzyme were characterized. Hydrolysis of carboxylmethylcellulose (CMC) by Umcel9A led to the decreased viscosity of CMC solution and production of reducing sugars. Interestingly, cellobiose was the major product when cellulosic materials were hydrolyzed by Umcel9A. Six representative carbohydrate-binding modules (CBMs) from different CBM families (CBM1, CBM2, CBM3, CBM4, CBM10, and CBM72) were fused with Umcel9A at the natural terminal position, resulting in significant enhancement of the binding capacity of the chimeric enzymes toward four different insoluble celluloses as compared with that of Umcel9A. Catalytic activity of the chimeric enzymes against insoluble celluloses, including phosphoric acid-swollen cellulose (PASC), alkali-pretreated sugarcane bagasse (ASB), filter paper powder (FPP), and Avicel, was higher than that of Umcel9A, except for Umcel9A-CBM3. In these chimeric enzymes, CBM4-Umcel9A exhibited the highest activity toward the four tested insoluble celluloses and displayed 4.2-, 3.0-, 2.4-, and 6.6-fold enhanced activity toward PASC, ASB, FPP, and Avicel, respectively, when compared with that of Umcel9A. CBM4-Umcel9A also showed highest V _max and catalytic efficiency (k _cat/K _M) against PASC. Construction of chimeric enzymes may have potential applications in biocatalytic processes and provides insight into the evolution of the molecular architecture of catalytic module and CBM in GH9 cellulases.     

Domain Analysis of a Modular α-l-Arabinofuranosidase with a Unique Carbohydrate Binding Strategy from the Fiber-Degrading Bacterium Fibrobacter succinogenes S85

Family 43 glycoside hydrolases (GH43s) are known to exhibit various activities involved in hemicellulose hydrolysis. Thus, these enzymes contribute to efficient plant cell wall degradation, a topic of much interest for biofuel production. In this study, we characterized a unique GH43 protein from Fibrobacter succinogenes S85. The recombinant protein showed α-l-arabinofuranosidase activity, specifically with arabinoxylan. The enzyme is, therefore, an arabinoxylan arabinofuranohydrolase (AXH). The F. succinogenes AXH (FSUAXH1) is a modular protein that is composed of a signal peptide, a GH43 catalytic module, a unique β-sandwich module (XX domain), a family 6 carbohydrate-binding module (CBM6), and F. succinogenes-specific paralogous module 1 (FPm-1). Truncational analysis and site-directed mutagenesis of the protein revealed that the GH43 domain/XX domain constitute a new form of carbohydrate-binding module and that residue Y484 in the XX domain is essential for binding to arabinoxylan, although protein structural analyses may be required to confirm some of the observations. Kinetic studies demonstrated that the Y484A mutation leads to a higher k_cat for a truncated derivative of FSUAXH1 composed of only the GH43 catalytic module and the XX domain. However, an increase in the K_m for arabinoxylan led to a 3-fold decrease in catalytic efficiency. Based on the knowledge that most XX domains are found only in GH43 proteins, the evolutionary relationships within the GH43 family were investigated. These analyses showed that in GH43 members with a XX domain, the two modules have coevolved and that the length of a loop within the XX domain may serve as an important determinant of substrate specificity.The plant cell wall is composed of a variety of polysaccharides and is the most abundant source of renewable biomass on our planet. There is an increasing effort to convert the cellulosic component to alcohols that can serve as biofuels. A critical step in this process is the enzymatic hydrolysis to release easily fermentable monomeric sugars, such as glucose and xylose, from the complex polysaccharides. However, the conversion of plant cell wall polysaccharides to biofuels is still far from being an ideal cost-effective process (53). Increasing the yields of enzymes during gene expression and bio-prospecting for enzymes with higher catalytic efficiencies are two strategies that can reduce the cost of production of biofuels. Ruminant animals have coevolved with a microbial consortium that harnesses enzymatic hydrolysis to release fermentable sugars from plant cell wall polysaccharides. The released sugars are subsequently fermented by the microbes to short-chain fatty acids that serve as the main energy source of the host (14, 33). Therefore, the genomes of plant cell wall-degrading microbes in the rumen represent a rich source of highly active plant cell wall-degrading enzymes. In addition, a better understanding of the strategies utilized by ruminal plant cell wall-degrading microorganisms should enhance rational design of enzymes with novel functions and/or improved activities through genetic engineering.The enzymes at the core of microbial plant cell wall degradation are the glycoside hydrolases (GHs). GHs frequently display a variety of modular structures. In addition to the catalytic domain, the most commonly observed module in glycoside hydrolases is the carbohydrate-binding module (CBM), which is known to enhance the accessibility of GHs to their appropriate polysaccharide substrates. Currently, there are 115 GH families and 59 CBM families in the carbohydrate active enzyme database (CAZy) (10), and combinations of these modules provide functional diversities to GHs.Hemicellulose is the second most abundant sugar polymer in the plant cell wall, and due to its heterogenous structure, it requires a set of at least five enzymes for its saccharification (12). The family 43 glycoside hydrolases (GH43s) are hemicellulolytic enzymes. They exhibit β-1,4-xylosidase (EC 3.2.1.37), β-1,3-xylosidase (EC 3.2.1.72), α-l-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), and galactan 1,3-β-galactosidase (EC 3.2.1.145) activities. Recent biophysical studies have revealed domain organizations and catalytic mechanisms in this family (3, 8, 9, 43, 65, 73). Based on their domain organization, these proteins are grouped into three different types. The first group includes 1,5-α-l-arabinanases from Cellvibrio japonicus (43), Bacillus thermodenitrificans (73), and Geobacillus stearothermophilus (3), and these proteins are composed of a single GH43 catalytic domain. The second group includes an arabinoxylan arabinofuranohydrolase enzyme from Bacillus subtilis (BsAXH-m2,3) and, in addition to the GH43 module, the proteins in this group have a family 6 carbohydrate-binding module (CBM6) at their C termini (65). The third group, which includes a β-xylosidase/α-l-arabinofuranosidase from the rumen bacterium Selenomonas ruminantium (SXA) (9) and a β-xylosidase from Geobacillus stearothermophilus (XynB3) (8), possesses in addition to the GH43 modules a C-terminally appended β-sandwich fold structure composed of approximately 200 amino acid residues. GH43 proteins of similar organization as SXA and XynB3 abound in the protein databases, and they are thought to form a cluster of orthologous group of proteins (COG) with β-xylosidase as their functional annotation. The large CBM-like β-sandwich structure in these proteins, however, lacks detailed biochemical characterization. Therefore, one of the aims of this study was to use both truncational and mutational analyses to probe the role of this module in the function of its associated GH43 module.Fibrobacter succinogenes S85 is a highly active cellulolytic ruminal bacterium (15). Interestingly, the genome of this bacterium also codes for many hemicellulolytic enzymes, despite its limited utilization of hemicellulose (41). To gain insight into this unusual metabolism, we have been studying a hemicellulolytic gene cluster that encodes more than 10 hemicellulose-targeting enzymes in the genome of F. succinogenes S85 (74). In this study, it is demonstrated that a GH43 modular protein (FSU2269) in the cluster (see Fig. S1 in the supplemental material) is an arabinoxylan arabinofuranohydrolase (AXH), which has been named FSUAXH1. Furthermore, the truncational and biochemical studies of this enzyme suggest that the unique β-sandwich domain (XX domain), which shares significant homology with the β-sandwich domains of SXA and XynB3, is important for binding to arabinoxylan. Since the majority of XX domains are only observed in GH43 proteins, we probed the relationship between the two different structural folds. The data presented here demonstrate interdependence between the two folds for substrate binding and suggest discovery of a new form of carbohydrate-binding module, likely composed of the interface between the GH43 module and the XX domain.     

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

The rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-l-arabinofuranosidase, β-d-xylosidase, α-l-arabinanase, and β-d-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides.     

Characterization of Five β-Glycoside Hydrolases from Cellulomonas fimi ATCC 484

The Gram-positive bacterium Cellulomonas fimi produces a large array of carbohydrate-active enzymes. Analysis of the collection of carbohydrate-active enzymes from the recent genome sequence of C. fimi ATCC 484 shows a large number of uncharacterized genes for glycoside hydrolase (GH) enzymes potentially involved in biomass utilization. To investigate the enzymatic activity of potential β-glucosidases in C. fimi, genes encoding several GH3 enzymes and one GH1 enzyme were cloned and recombinant proteins were expressed in Escherichia coli. Biochemical analysis of these proteins revealed that the enzymes exhibited different substrate specificities for para-nitrophenol-linked substrates (pNP), disaccharides, and oligosaccharides. Celf_2726 encoded a bifunctional enzyme with β-d-xylopyranosidase and α-l-arabinofuranosidase activities, based on pNP-linked substrates (CfXyl3A). Celf_0140 encoded a β-d-glucosidase with activity on β-1,3- and β-1,6-linked glucosyl disaccharides as well as pNP-β-Glc (CfBgl3A). Celf_0468 encoded a β-d-glucosidase with hydrolysis of pNP-β-Glc and hydrolysis/transglycosylation activities only on β-1,6-linked glucosyl disaccharide (CfBgl3B). Celf_3372 encoded a GH3 family member with broad aryl-β-d-glycosidase substrate specificity. Celf_2783 encoded the GH1 family member (CfBgl1), which was found to hydrolyze pNP-β-Glc/Fuc/Gal, as well as cellotetraose and cellopentaose. CfBgl1 also had good activity on β-1,2- and β-1,3-linked disaccharides but had only very weak activity on β-1,4/6-linked glucose.     

Cel9D, an atypical 1,4-beta-D-glucan glucohydrolase from Fibrobacter succinogenes: characteristics, catalytic residues, and synergistic interactions with other cellulases

The increasing demands of renewable energy have led to the critical emphasis on novel enzymes to enhance cellulose biodegradation for biomass conversion. To identify new cellulases in the ruminal bacterium Fibrobacter succinogenes, a cell extract of cellulose-grown cells was separated by ion-exchange chromatography and cellulases were located by zymogram analysis and identified by peptide mass fingerprinting. An atypical family 9 glycoside hydrolase (GH9), Cel9D, with less than 20% identity to typical GH9 cellulases, was identified. Purified recombinant Cel9D enhanced the production of reducing sugar from acid swollen cellulose (ASC) and Avicel by 1.5- to 4-fold when mixed separately with each of four other glucanases, although it had low activity on these substrates. Cel9D degraded ASC and cellodextrins with a degree of polymerization higher than 2 to glucose with no apparent endoglucanase activity, and its activity was restricted to beta-1-->4-linked glucose residues. It catalyzed the hydrolysis of cellulose by an inverting mode of reaction, releasing glucose from the nonreducing end. Unlike many GH9 cellulases, calcium ions were not required for its function. Cel9D had increased kcat/Km values for cello-oligosaccharides with higher degrees of polymerization. The kcat/Km value for cellohexaose was 2,300 times higher than that on cellobiose. This result indicates that Cel9D is a 1,4-beta-D-glucan glucohydrolase (EC 3.2.1.74) in the GH9 family. Site-directed mutagenesis of Cel9D identified Asp166 and Glu612 as the candidate catalytic residues, while Ser168, which is not present in typical GH9 cellulases, has a crucial structural role. This enzyme has an important role in crystalline cellulose digestion by releasing glucose from accessible cello-oligosaccharides.