Towards designer cellulosomes in Clostridia: mannanase enrichment of the cellulosomes produced by Clostridium cellulolyticum

The man5K gene of Clostridium cellulolyticum was cloned and overexpressed in Escherichia coli. This gene encodes a 424-amino-acid preprotein composed of an N-terminal leader peptide, followed by a dockerin module and a C-terminal catalytic module belonging to family 5 of the glycosyl hydrolases. Mature Man5K displays 62% identity with ManA from Clostridium cellulovorans. Two forms of the protein were purified from E. coli; one form corresponds to the full-length enzyme (45 kDa), and a truncated form (39 kDa) lacks the N-terminal dockerin module. Both forms exhibit the same typical family 5 mannanase substrate preference; they are very active with the galactomannan locust bean gum, and the more galacto-substituted guar gum molecules are degraded less. The truncated form, however, displays fourfold-higher activity with galactomannans than the full-length enzyme. Man5K was successfully overproduced in C. cellulolyticum by using expression vectors. The trans-produced protein was found to be incorporated into the cellulosomes and became one of the major enzymatic components. Modified cellulosomes displayed 20-fold-higher specific activities than control fractions on galactomannan substrates, whereas the specific activity on crystalline cellulose was reduced by 20%. This work clearly showed that the composition of the cellulosomes is obviously regulated by the relative amounts of the enzymes produced and that this composition can be engineered in clostridia by structural gene cloning.     

Determination of subunit composition of Clostridium cellulovorans cellulosomes that degrade plant cell walls

Clostridium cellulovorans produces a cellulase enzyme complex (cellulosome). In this study, we isolated two plant cell wall-degrading cellulosomal fractions from culture supernatant of C. cellulovorans and determined their subunit compositions and enzymatic activities. One of the cellulosomal fractions showed fourfold-higher plant cell wall-degrading activity than the other. Both cellulosomal fractions contained the same nine subunits (the scaffolding protein CbpA, endoglucanases EngE and EngK, cellobiohydrolase ExgS, xylanase XynA, mannanase ManA, and three unknown proteins), although the relative amounts of the subunits differed. Since only cellobiose was released from plant cell walls by the cellulosomal fractions, cellobiohydrolases were considered to be key enzymes for plant cell wall degradation.     

Adhesion of Clostridium cellulolyticum spores to filter paper

The adhesion of Clostridium cellulolyticum spores and cells to Whatman No. 1 filter paper was studied. A suspension of vegetative cells in exponential phase from a culture on cellobiose adhered at 60% whereas spores at the same initial concentration were bound to the Whatman filter paper at 90%. Adhesion of vegetative cellulolytic cells occurs on specific cellulosic sites and reveals a sigmoid type II curve. Non-cellulolytic vegetative cells from Clostridium butyricum do not adhere to the cellulose. Spore adhesion is a non-specific process since non-cellulolytic spores from Clostridium butyricum adhered almost in the same range to filter paper than cellulolytic spores.     

Colonization of Crystalline Cellulose by Clostridium cellulolyticum ATCC 35319

Cellulose colonization by Clostridium cellulolyticum was studied by using [methyl-³H]thymidine incorporation. The colonization process indicated that a part of the bacterial population was released from cellulose to the liquid phase before binding and colonizing another adhesion site of the cellulose. We postulate that cellulose colonization occurs according to the following process: adhesion, colonization, release, and readhesion.     

Improvement of Cellulolytic Properties of Clostridium cellulolyticum by Metabolic Engineering

Cellulolytic clostridia have evolved to catabolize lignocellulosic materials at a seasonal biorhythm, so their biotechnological exploitation requires genetic improvements. As high carbon flux leads to pyruvate accumulation, which is responsible for the cessation of growth of Clostridium cellulolyticum, this accumulation is decreased by heterologous expression of pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis. In comparison with that of the wild strain, growth of the recombinant strain at the same specific rate but for 145 h instead of 80 h led to a 150% increase in cellulose consumption and a 180% increase in cell dry weight. The fermentation pattern was shifted significantly: lactate production decreased by 48%, whereas the concentrations of acetate and ethanol increased by 93 and 53%, respectively. This study demonstrates that the fermentation of cellulose, the most abundant and renewable polymer on earth, can be greatly improved by using genetically engineered C. cellulolyticum.     

Metabolism and Solubilization of Cellulose by Clostridium cellulolyticum H10

When Clostridium cellulolyticum was grown with cellulose MN300 as the substrate, the rates of growth and metabolite production were found to be lower than those observed with soluble sugars as the substrate. At low cellulose concentrations, the growth yields were equal to those obtained with cellobiose. The main fermentation products from cellulose and soluble sugars were the same. Up to 15 mM of consumed hexose, a change in the metabolic pathway favoring lactate production similar to that observed with soluble sugars was found to occur concomitantly with a decrease in molar growth yield. With cellulose concentrations above 5 g/liter, accumulation of soluble sugars occurred once growth had ceased. Glucose accounted for 30% of these sugars. A kinetic analysis of cellulose solubilization revealed that cellulolysis by C. cellulolyticum involved three stages whatever cellulose concentration was used. Analysis of these kinetics showed three consecutive enzymatic activity levels having the same K_m (0.8 g of cellulose per liter, i.e., 5 mM hexose equivalent) but decreasing values of V_max. The hypothesis is suggested that each step corresponds to differences in cellulose structure.     

A rhamnogalacturonan lyase in the Clostridium cellulolyticum cellulosome

Clostridium cellulolyticum secretes large multienzymatic complexes with plant cell wall-degrading activities named cellulosomes. Most of the genes encoding cellulosomal components are located in a large gene cluster: cipC-cel48F-cel8C-cel9G-cel9E-orfX-cel9H-cel9J-man5K-cel9M. Downstream of the cel9M gene, a new open reading frame was discovered and named rgl11Y. Amino acid sequence analysis indicates that this gene encodes a multidomain pectinase, Rgl11Y, containing an N-terminal signal sequence, a catalytic domain belonging to family 11 of the polysaccharide lyases, and a C-terminal dockerin domain. The present report describes the biochemical characterization of a recombinant form of Rgl11Y. Rgl11Y cleaves the alpha-L-Rhap-(1-->4)-alpha-D-GalpA glycosidic bond in the backbone of rhamnogalacturonan I (RGI) via a beta-elimination mechanism. Its specific activity on potato pectic galactan and rhamnogalacturonan was found to be 28 and 3.6 IU/mg, respectively, indicating that Rgl11Y requires galactan decoration of the RGI backbone. The optimal pH of Rgl11Y is 8.5 and calcium is required for its activity. Rgl11Y was shown to be incorporated in the C. cellulolyticum cellulosome through a typical cohesin-dockerin interaction. Rgl11Y from C. cellulolyticum is the first cellulosomal rhamnogalacturonase characterized.     

解纤维梭菌培养条件的优化

解纤维梭菌Clostridium cellulolyticum是产纤维小体的专性厌氧菌,由于其培养困难,目前仍难以实现高效培养.文中采用响应面法对产纤维小体的解纤维梭菌C.cellulolyticum高细胞密度培养的条件进行了优化.首先用Plackett-Burman实验设计对影响因素效应进行评价,筛选出的显著影响因素分别为:酵母提取物浓度、纤维二糖浓度及培养温度.之后用最陡爬坡实验设计逼近菌体最佳生长条件的区域范围.最后通过中心组合实验设计和响应面分析方法确定显著影响因素的水平和C.cellulolyticum的最优培养条件.优化后的显著影响因素酵母提取物浓度、纤维二糖浓度和培养温度分别为3 g/L、7 g/L和34℃.在最优条件下,摇瓶培养的菌体浓度OD600值由0.303提高到了0.586,增加了93.4％.在发酵罐批次培养条件下,菌体OD600值达到了3.432,比文献报道值高出了2.8倍.研究结果为C.cellulolyticum培养及应用研究提供了基础.     

Improvement of cellulolytic properties of Clostridium cellulolyticum by metabolic engineering.

Cellulolytic clostridia have evolved to catabolize lignocellulosic materials at a seasonal biorhythm, so their biotechnological exploitation requires genetic improvements. As high carbon flux leads to pyruvate accumulation, which is responsible for the cessation of growth of Clostridium cellulolyticum, this accumulation is decreased by heterologous expression of pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis. In comparison with that of the wild strain, growth of the recombinant strain at the same specific rate but for 145 h instead of 80 h led to a 150% increase in cellulose consumption and a 180% increase in cell dry weight. The fermentation pattern was shifted significantly: lactate production decreased by 48%, whereas the concentrations of acetate and ethanol increased by 93 and 53%, respectively. This study demonstrates that the fermentation of cellulose, the most abundant and renewable polymer on earth, can be greatly improved by using genetically engineered C. cellulolyticum.     

Random Mutagenesis of Clostridium cellulolyticum by Using a Tn1545 Derivative

Further understanding of the plant cell wall degradation system of Clostridium cellulolyticum and the possibility of metabolic engineering in this species highlight the need for a means of random mutagenesis. Here, we report the construction of a Tn1545-derived delivery tool which allows monocopy random insertion within the genome.The economic feasibility and sustainability of lignocellulosic ethanol production are dependent on the development of robust microorganisms which can efficiently degrade and/or convert plant biomass to ethanol (5). The anaerobic, mesophilic, Gram-positive bacterium Clostridium cellulolyticum is a candidate microorganism, as it is capable of hydrolyzing plant cell wall polysaccharides and fermenting the hydrolysis products to ethanol and other metabolites (7). C. cellulolyticum achieves this efficient hydrolysis by using multiprotein extracellular enzymatic complexes, termed cellulosomes (13). As plant cell walls consist of several intertwined heterogeneous polymers, primarily composed of cellulose, hemicellulose, and pectin, cellulosomes contain many subunits (cellulosomal enzymes) with diverse and complementary enzymatic properties (2). Thus, this model organism is also a good candidate for the development of novel and efficient cellulases and hemicellulases for the saccharification of plant biomass.Gene transfer has been successfully carried out in C. cellulolyticum (8, 12). This possibility has allowed the in vivo function of cellulosomal enzymes in C. cellulolyticum to be examined by overexpression (9) or down expression (11) of targeted genes. However, random mutagenesis of the entire chromosome and screening of mutants to identify key components for plant cell wall degradation have never been described. Conjugative transfer of Tn1545 from Enterococcus faecalis to C. cellulolyticum has been described but is limited by low transfer frequency and poor reproducibility (8). To improve transposon mutagenesis of C. cellulolyticum, we exploited the two-plasmid Tn1545 delivery system described by Trieu-Cuot et al. (15). In this system, the Tn916 integrase-encoding gene is carried by an expression vector, whereas the attachment site of Tn1545 is carried by a suicide vector. Tn916 and Tn1545 being closely related (4), integration of the Tn1545 derivative occurs in the genome after transformation of the strain with both vectors (15).     

Modulation of cellulosome composition in Clostridium cellulolyticum: Adaptation to the polysaccharide environment revealed by proteomic and carbohydrate‐active enzyme analyses

Clostridium cellulolyticum is a model mesophilic anaerobic bacterium that efficiently degrades plant cell walls. The recent genome release offers the opportunity to analyse its complete degradation system. A total of 148 putative carbohydrate‐active enzymes were identified, and their modular structures and activities were predicted. Among them, 62 dockerin‐containing proteins bear catalytic modules from numerous carbohydrate‐active enzymes' families and whose diversity reflects the chemical and structural complexity of the plant carbohydrate. The composition of the cellulosomes produced by C. cellulolyticum upon growth on different substrates (cellulose, xylan, and wheat straw) was investigated by LC MS/MS. The majority of the proteins encoded by the cip‐cel operon, essential for cellulose degradation, were detected in all cellulosome preparations. In the presence of wheat straw, the natural and most complex of the substrates studied, additional proteins predicted to be involved in hemicellulose degradation were produced. A 32‐kb gene cluster encodes the majority of these proteins, all harbouring carbohydrate‐binding module 6 or carbohydrate‐binding module 22 xylan‐binding modules along dockerins. This newly identified xyl‐doc gene cluster, specialised in hemicellulose degradation, comes in addition of the cip‐cel operon for plant cell wall degradation. Hydrolysis efficiencies determined on the different substrates corroborates the finding that cellulosome composition is adapted to the growth substrate.     

Enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum explored by two-dimensional analysis: identification of seven genes encoding new dockerin-containing proteins

The enzyme diversity of the cellulolytic system produced by Clostridium cellulolyticum grown on crystalline cellulose as a sole carbon and energy source was explored by two-dimensional electrophoresis. The cellulolytic system of C. cellulolyticum is composed of at least 30 dockerin-containing proteins (designated cellulosomal proteins) and 30 noncellulosomal components. Most of the known cellulosomal proteins, including CipC, Cel48F, Cel8C, Cel9G, Cel9E, Man5K, Cel9M, and Cel5A, were identified by using two-dimensional Western blot analysis with specific antibodies, whereas Cel5N, Cel9J, and Cel44O were identified by using N-terminal sequencing. Unknown enzymes having carboxymethyl cellulase or xylanase activities were detected by zymogram analysis of two-dimensional gels. Some of these enzymes were identified by N-terminal sequencing as homologs of proteins listed in the NCBI database. Using Trap-Dock PCR and DNA walking, seven genes encoding new dockerin-containing proteins were cloned and sequenced. Some of these genes are clustered. Enzymes encoded by these genes belong to glycoside hydrolase families GH2, GH9, GH10, GH26, GH27, and GH59. Except for members of family GH9, which contains only cellulases, the new modular glycoside hydrolases discovered in this work could be involved in the degradation of different hemicellulosic substrates, such as xylan or galactomannan.     

Lipids and fatty acids in cellulosomes of Clostridium thermocellum

A lipid component was found in cellulosomes (multienzymatic cellulase complexes) of the thermophilic bacterium Clostridium thermocellum. Two major fractions of the cellulosomes have been studied, one with a relative molecular mass (M_r) of 10–50 million (polycellulosomes, fraction A) and the other with an M_r 0.5–10 million (fraction B) It was found that the larger cellulosomes contained higher relative amounts of lipids (8.1%) as well as Ca²⁺ ions (0.6%), and showed higher cellulolytic activity Among the lipids was cardiolipin, 1,2- and 1,3-diglycerides, triglycerides, and up to 11 free fatty acids, including both saturated (palmitic, lauric, myristic, pentadecanoic, stearic, arachinic) and unsaturated (myristoleic, palmitoleic, and oleic) moieies Cardiolipin was a major phospholipid component in cellulosomes and was also found to be a major phospholipid component of the cell membrane, palmitic acid was a major fatty acid Fraction B contained less fatty acids (0.5% vs 1.27% in fraction A) with fewer acids detected than in fraction A Removal of the extractable lipids led to fragmentation of the cellulosomes with a concurrent sharp drop in their enzymatic activity Total removal of the lipids from cellulosomes was possible only when the proteins were completely denatured The qualitative composition of the extractable and non-extractable fatty acids was the same The lipid component of the cellulosomes, containing a high content of the unsaturated fatty acids, was located mainly in the part of cellulosomes that is in tight contact with the cellulose surface, and it apparently plays an important role in the tight adsorption of the cellulosomes on cellulose.     

Cellulose promotes extracellular assembly of Clostridium cellulovorans cellulosomes.

Cellulosome synthesis by Clostridium cellulovorans was investigated by growing the cells in media containing different carbon sources. Supernatant from cells grown with cellobiose contained no cellulosomes and only the free forms of cellulosomal major subunits CbpA, P100, and P70 and the minor subunits with enzymatic activity. Supernatant from cells grown on pebble-milled cellulose and Avicel contained cellulosomes capable of degrading crystalline cellulose. Supernatants from cells grown with cellobiose, pebble-milled cellulose, and Avicel contained about the same amount of carboxymethyl cellulase activity. Although the supernatant from the medium containing cellobiose did not initially contain active cellulosomes, the addition of crystalline cellulose to the cell-free supernatant fraction converted the free major forms to cellulosomes with the ability to degrade crystalline cellulose. The binding of P100 and P70 to crystalline cellulose was dependent on their attachment to the endoglucanase-binding domains of CbpA. These data strongly indicate that crystalline cellulose promotes cellulosome assembly.     

Characterization of endoglucanase A from Clostridium cellulolyticum.

A construction was carried out to obtain a high level of expression in Escherichia coli of the gene celCCA, coding for the endoglucanase A from Clostridium cellulolyticum (EGCCA). The enzyme was purified in two forms with different molecular weights, 51,000 and 44,000. The smaller protein was probably the result of proteolysis, although great care was taken to prevent this process from occurring. Evidence was found for the loss of the conserved reiterated domains which are characteristic of C. thermocellum and C. cellulolyticum cellulases. The two forms were extensively studied, and it was demonstrated that although they had the same pH and temperature optima, they differed in their catalytic properties. The truncated protein gave the more efficient catalytic parameters on carboxymethyl cellulose and showed improved endoglucanase characteristics, whereas the intact enzyme showed truer cellulase characteristics. The possible role of clostridial reiterated domains in the hydrolytic activity toward crystalline cellulose is discussed.     

Sequence analysis of the Clostridium cellulolyticum endoglucanase-A-encoding gene, celCCA

The nucleotide sequence of a Clostridium cellulolyticum endo-beta-1,4- glucanase (EGCCA)-encoding gene (celCCA) and its flanking regions, was determined. An open reading frame (ORF) of 1425 bp was found, encoding a protein of 475 amino acids (aa). This ORF began with an ATG start codon and ended with a TAA ochre stop codon. The N-terminal region of the EGCCA protein resembled a typical signal sequence of a Gram-positive bacterial extracellular protein. A putative signal peptidase cleavage site was determined. EGCCA, without a signal peptide, was found to be composed of more than 35% hydrophobic aa and to have an Mr of 50715. Comparison of the encoded sequence with other known cellulase sequences showed the existence of various kinds of aa sequence homologies. First, a strong homology was found between the C-terminal region of EGCCA, containing a reiterated stretch of 24 aa, and the conserved reiterated region previously found to exist in four Clostridium thermocellum endoglucanases and one xylanase from the same organism. This region was suspected of playing a role in organizing the cellulosome complex. Second, an extensive homology was found between EGCCA and the N-terminal region of the large endoglucanase, EGE, from C. thermocellum, which suggests that they may have a common ancestral gene. Third, a region, which extended for 21 aa residues beginning at aa + 127, was found to be homologous with regions of cellulases belonging to Bacilli, Clostridia and Erwinia chrysanthemi.