Functional characterization of the galactan utilization system of Geobacillus stearothermophilu.
Tabachnikov, O. & Shoham, Y. (2013). FEBS Journal, 280(3), 950–964.
Type I galactan is a pectic polysaccharide composed of β-1,4 linked units of D-galactose and is part of the main plant cell wall polysaccharides, which are the most abundant sources of renewable carbon in the biosphere. The thermophilic bacterium Geobacillus stearothermophilus T-6 possesses an extensive system for the utilization of plant cell wall polysaccharides, including a 9.4-kb gene cluster, ganREFGBA, which encodes galactan-utilization elements. Based on enzyme activity assays, the ganEFGBA genes, which probably constitute an operon, are induced by short galactosaccharides but not by galactose. GanA is a glycoside hydrolase family 53 β-1,4-galactanase, active on high molecular weight galactan, producing galactotetraose as the main product. Homology modelling of the active site residues suggests that the enzyme can accommodate at least eight galactose molecules (at subsites −4 to +4) in the active site. GanB is a glycoside hydrolase family 42 β-galactosidase capable of hydrolyzing short β-1,4 galactosaccharides into galactose. Applying both GanA and GanB on galactan resulted in the full degradation of the polymer into galactose. The ganEFG genes encode an ATP-binding cassette sugar transport system whose sugar-binding lipoprotein, GanE, was shown to bind galacto-oligosaccharides. The utilization of galactan by G. stearothermophilus involves the extracellular galactanase GanA cleaving galactan into galacto-oligosaccharides that enter the cell via a specific transport system GanEFG. The galacto-oligosaccharides are further degraded by the intracellular β-galactosidase GanB into galactose, which is then metabolized into UDP-glucose via the Leloir pathway by the galKET gene products.
Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization.
Ochiai, A., Itoh, T., Kawamata, A., Hashimoto, W. & Murata, K. (2007). Applied and Environmental Microbiology, 73(12), 3803-3813.
Plant cell wall degradation is a premier event when Bacillus subtilis, a typical saprophytic bacterium, invades plants. Here we show the degradation system of rhamnogalacturonan type I (RG-I), a component of pectin from the plant cell wall, in B. subtilis strain 168. Strain 168 cells showed a significant growth on plant cell wall polysaccharides such as pectin, polygalacturonan, and RG-I as a carbon source. DNA microarray analysis indicated that three gene clusters (yesOPQRSTUVWXYZ, ytePQRST, and ybcMOPST-ybdABDE) are inducibly expressed in strain 168 cells grown on RG-I. Cells of an industrially important bacterium, B. subtilis strain natto, fermenting soybeans also express the gene cluster including the yes series during the assimilation of soybean used as a carbon source. Among proteins encoded in the yes cluster, YesW and YesX were found to be novel types of RG lyases releasing disaccharide from RG-I. Genetic and enzymatic properties of YesW and YesX suggest that strain 168 cells secrete YesW, which catalyzes the initial cleavage of the RG-I main chain, and the resultant oligosaccharides are converted to disaccharides through the extracellular exotype YesX reaction. The disaccharide is finally degraded into its constituent monosaccharides through the reaction of intracellular unsaturated galacturonyl hydrolases YesR and YteR. This enzymatic route for RG-I degradation in strain 168 differs significantly from that in plant-pathogenic fungus Aspergillus aculeatus. This is, to our knowledge, the first report on the bacterial system for complete RG-I main chain degradation.
A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.
McKie, V. A., Vincken, J. P., Voragen, A. G. J., van den Broek, L. A. M., Stimson, E. & Gilbert, H. J. (2001). Biochem. J, 355(1), 167-177.
Pseudomonas cellulosa is an aerobic bacterium that synthesizes an extensive array of modular cellulases and hemicellulases, which have a modular architecture consisting of catalytic domains and distinct non-catalytic carbohydrate-binding modules (CBMs). To investigate whether the main-chain-cleaving pectinases from this bacterium also have a modular structure, a library of P. cellulosa genomic DNA, constructed in λZAPII, was screened for pectinase-encoding sequences. A recombinant phage that attacked arabinan, galactan and rhamnogalacturonan was isolated. The encoded enzyme, designated Rgl11A, had a modular structure comprising an N-terminal domain that exhibited homology to Bacillus and Streptomyces proteins of unknown function, a middle domain that exhibited sequence identity to fibronectin-3 domains, and a C-terminal domain that was homologous to family 2a CBMs. Expression of the three modules of the Pseudomonas protein in Escherichia coli showed that its C-terminal module was a functional cellulose-binding domain, and the N-terminal module consisted of a catalytic domain that hydrolysed rhamnogalacturonan-containing substrates. The activity of Rgl11A against apple- and potato-derived rhamnogalacturonan substrates indicated that the enzyme had a strong preference for rhamnogalacturonans that contained galactose side chains, and which were not esterified. The enzyme had an absolute requirement for calcium, a high optimum pH, and catalysis was associated with an increase in absorbance at 235nm, indicating that glycosidic bond cleavage was mediated via a β-elimination mechanism. These data indicate that Rgl11A is a rhamnogalacturonan lyase and, together with the homologous Bacillus and Streptomyces proteins, comprise a new family of polysaccharide lyases. The presence of a family 2a CBM in Rgl11A, and in a P. cellulosa pectate lyase described in the accompanying paper [Brown, Mallen, Charnock, Davies and Black (2001) Biochem. J. 355, 155–165] suggests that the capacity to bind cellulose plays an important role in the activity of main-chain-cleaving Pseudomonas pectinases, in addition to cellulases and hemicellulases.
Characterization of the Erwinia chrysanthemi gan locus, involved in galactan catabolism.
Delangle, A., Prouvost, A. F., Cogez, V., Bohin, J. P., Lacroix, J. M. & Cotte-Pattat, N. H. (2007). Journal of Bacteriology, 189(19), 7053-7061.
β-1,4-Galactan is a major component of the ramified regions of pectin. Analysis of the genome of the plant pathogenic bacteria Erwinia chrysanthemi revealed the presence of a cluster of eight genes encoding proteins potentially involved in galactan utilization. The predicted transport system would comprise a specific porin GanL and an ABC transporter made of four proteins, GanFGK2. Degradation of galactans would be catalyzed by the periplasmic 1,4-β-endogalactanase GanA, which released oligogalactans from trimer to hexamer. After their transport through the inner membrane, oligogalactans would be degraded into galactose by the cytoplasmic 1,4-β-exogalactanase GanB. Mutants affected for the porin or endogalactanase were unable to grow on galactans, but they grew on galactose and on a mixture of galactotriose, galactotetraose, galactopentaose, and galactohexaose. Mutants affected for the periplasmic galactan binding protein, the transporter ATPase, or the exogalactanase were only able to grow on galactose. Thus, the phenotypes of these mutants confirmed the functionality of the gan locus in transport and catabolism of galactans. These mutations did not affect the virulence of E. chrysanthemi on chicory leaves, potato tubers, or Saintpaulia ionantha, suggesting an accessory role of galactan utilization in the bacterial pathogeny.
The β-1,4‐endogalactanase A gene from Aspergillus niger is specifically induced on arabinose and galacturonic acid and plays an important role in the degradation of pectic hairy regions.
de Vries, R. P., Pařenicová, L., Hinz, S. W. A., Kester, H. C. M., Beldman, G., Benen, J. A. E. & Visser, J. (2002). European Journal of Biochemistry, 269(20), 4985-4993.
The Aspergillus niger β-1,4-endogalactanase encoding gene (galA) was cloned and characterized. The expression of galA in A. niger was only detected in the presence of sugar beet pectin, D-galacturonic acid and L-arabinose, suggesting that galA is coregulated with both the pectinolytic genes as well as the arabinanolytic genes. The corresponding enzyme, endogalactanase A (GALA), contains both active site residues identified previously for the Pseudomonas fluorescens β-1,4-endogalactanase. The galA gene was overexpressed to facilitate purification of GALA. The enzyme has a molecular mass of 48.5 kDa and a pH optimum between 4 and 4.5. Incubations of arabinogalactans of potato, onion and soy with GALA resulted initially in the release of D-galactotriose and D-galactotetraose, whereas prolonged incubation resulted in D-galactose and D-galactobiose, predominantly. MALDI-TOF analysis revealed the release of L-arabinose substituted D-galactooligosaccharides from soy arabinogalactan. This is the first report of the ability of a β-1,4-endogalactanase to release substituted D-galacto-oligosaccharides. GALA was not active towards D-galacto-oligosaccharides that were substituted with D-glucose at the reducing end.
Evidence that galactanase A from Pseudomonas fluorescens subspecies cellulosa is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues.
Braithwaite, K. L., Barna, T., Spurway, T. D., Charnock, S. J., Black, G. W., Hughes, N., Lakey, J. H., Virden, R., Hazelwood, G. P., Henrissat, B. & Gilbert, H. J. (1997). Biochemistry, 36(49), 15489-15500.
A genomic library of Pseudomonas fluorescens subsp. cellulosa DNA was screened for galactanase-positive recombinants. The nine galactanase positive phage isolated contained the same galactanase gene designated galA. The deduced primary structure of the enzyme (galactanase A; GalA) encoded by galA had a Mr of 42 130 and exhibited significant sequence identity with a galactanase from Aspergillus aculeatus, placing GalA in glycosyl hydrolase family 53. The enzyme displayed properties typical of an endo-β1,4-galactanase and exhibited no activity against the other plant structural polysaccharides evaluated. Analysis of the stereochemical course of 2,4-dinitrophenyl-β-galactobioside (2,4-DNPG2) hydrolysis by GalA indicated that the galactanase catalyzes the hydrolysis of glycosidic bonds by a double displacement general acid−base mechanism. Hydrophobic cluster analysis (HCA) suggested that family 53 enzymes are related to the GH-A clan of glycosyl hydrolases, which have an (α)/β) 8 barrel structure. HCA also predicted that E161 and E270 were the acid−base and nucleophilic residues, respectively. Mutants of GalA in which E161 and E270 had been replaced with alanine residues were essentially inactive against galactan. Against 2,4-DNPG2, E161A exhibited a much lower Km and kcat than native GalA, while E270A was inactive against the substrate. Analysis of the pre-steady-state kinetics of 2,4-DNPG2 hydrolysis by E161A showed that there was an initial rapid release of 2,4-dinitrophenol (2,4-DNP), which then decayed to a slow steady-state rate of product formation. No pre-steady-state burst of 2,4-DNP release was observed with the wild-type enzyme. These data are consistent with the HCA prediction that E161 and E270 are the acid−base and nucleophilic catalytic residues of GalA, respectively.
A simple assay procedure for β-D-mannanase.
McCleary, B. V. (1978). Carbohydrate Research, 67(1), 213-221.
A simple assay procedure for β-D-mannanase enzyme has been developed which employs carob D-galacto-D-mannan dyed with Remazolbrilliant Blue. Additionally, the procedure is quantitative, relatively sensitive, and highly specific for β-D-mannanase enzyme. It can be readily used for the determination of β-D-mannanase activity in crude enzyme preparations and column-chromatography eluates.