Cloning and characterization of arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis DSM20083.
Van den Broek, L. A. M., Lloyd, R. M., Beldman, G., Verdoes, J. C., McCleary, B. V. & Voragen, A. G. J. (2005). Applied Microbiology and Biotechnology, 67(5), 641-647.
Arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis
releases only C3-linked arabinose residues from double-substituted xylose residues. A genomic library of B. adolescentis DSM20083 was screened for the presence of the axhD3 gene. Two plasmids were identified containing part of the axhD3 gene. The nucleotide sequences were combined and three open reading frames (ORFs) were found. The first ORF showed high homology with xylanases belonging to family 8 of the glycoside hydrolases and this gene was designated xylA. The second ORF was the axhD3 gene belonging to glycoside hydrolase family 43. The third (partial) ORF coded for a putative carboxylesterase. The axhD3 gene was cloned and expressed in Escherichia coli. Several substrates were employed in the biochemical characterization of recombinant AXHd3. The enzyme showed the highest activity toward wheat arabinoxylan oligosaccharides. In addition, β-xylanase from Trichoderma sp. was able to degrade soluble wheat arabinoxylan polymer to a higher extent, after pretreatment with recombinant AXHd3. Arabinoxylan oligosaccharides incubated with a combination of recombinant AXHd3 and an α-L-arabinofuranosidase from Aspergillus niger did not result in a higher maximal release of arabinose than incubation with these enzymes separately.
Extracellular arabinases in Aspergillus nidulans: the effect of different cre mutations on enzyme levels.
Van der Veen, P., Arst Jr, H. N., Flipphi, M. J. & Visser, J. (1994). Archives of Microbiology, 162(6), 433-440.
The regulation of the syntheses of two arabinan-degrading extracellular enzymes and several intracellular L-arabinose catabolic enzymes was examined in wild-type and carbon catabolite derepressed mutants of Aspergillus nidulans. α-L-Arabinofuranosidase B, endoarabinase, L-arabinose reductase, L-arabitol dehydrogenase, xylitol dehydrogenase, and L-xylulose reductase were all inducible to varying degrees by L-arabinose and L-arabitol and subject to carbon catabolite repression by D-glucose. With the exception of L-xylulose reductase, all were clearly under the control of creA, a negative-acting wide domain regulatory gene mediating carbon catabolite repression. Measurements of intracellular enzyme activities and of intracellular concentrations of arabitol and xylitol in mycelia grown on D-glucose in the presence of inducer indicated that carbon catabolite repression diminishes, but does not prevent uptake of inducer. Mutations in creA resulted in an apparently, in some instances very marked, elevated inducibility, perhaps reflecting an element of “self” catabolite repression by the inducing substrate. creA mutations also resulted in carbon catabolite derepression to varying degrees. The regulatory effects of a mutation in creB and in creC, two genes whose roles are unclear, but likely to be indirect, were, when observable, more modest. As with previous data showing the effect of creA mutations on structural gene expression, there were striking instances of phenotypic variation amongst creA mutant alleles and this variation followed no discernible pattern, i.e. it was non-hierarchical. This further supports molecular data obtained elsewhere, indicating a direct role for creA in regulating structural gene expression, and extends the range of activities under creA control.
Molecular cloning, expression and structure of the endo-1,5-α-L-arabinase gene of Aspergillus niger.
Flipphi, M. J. A., Panneman, H., van der Veen, P., Visser, J. & de Graaff, L. H. (1993). Applied Microbiology and Biotechnology, 40(2-3), 318-326.
Secretion of endo-1,5-α-L-arabinase A (ABNA) by an Aspergillus niger xylulose kinase mutant upon mycelium transfer to medium containing L-arabitol was immunochemically followed with time to monitor its induction profile. A cDNA expression library was made from polyA+ RNA isolated from the induced mycelium. This library was immunochemically screened and one ABN A specific clone emerged. The corresponding abnA gene was isolated from an A. niger genomic library. Upon Southern blot analysis, a 3.1-kb HindIII fragment was identified and subcloned to result in plasmid pIM950. By means of co-tranformation using the A. niger pyrA gene as selection marker, the gene was introduced in both A. niger and A. nidulans uridine auxotrophic mutants. Prototrophic A. niger and A. nidulans transformants overproduced A. niger ABN A upon growth in medium containing sugar beet pulp as the sole carbon source, thereby establishing the identity and functionality of the cloned gene. The DNA sequence of the complete HindIII fragment was determined and the structure of the abnA gene as well as of its deduced gene product were analysed. Gene abnA contains three introns within its structural region and codes for a protein of 321 amino acids. Signal peptide processing results in a mature protein of 302 amino acids with a deduced molecular mass of 32.5 kDa. A. niger abnA is the first gene encoding an ABN to be isolated and characterized.
Efficient production of protopectinases by Bacillus subtilis using medium based on soybean flour.
Matsumoto, T., Sugiura, Y., Kondo, A. & Fukuda, H. (2000). Biochemical Engineering Journal, 6(2), 81-86.
We have developed a culture system for efficient production of protopectinases (PPases) by Bacillus subtilis. PPase shows the pectin-releasing activity and is expected to be utilized in the enzymatic cotton scouring. B. subtilis IFO3134 was cultivated using defatted soybean flour as a main component of culture media. This strain produced three different types of PPases, namely, PPase-C, -N and -R performing endo-arabinase activity, pectate-lyase activity and pectin-lyase activity, respectively. The effects of alkaline solubilization and autoclave treatments to extract nutrients from soybean flour and initial soybean flour concentration (20–80 g/l) on production of PPases in batch fermentation were investigated. Alkaline solubilization of soybean flour with NaOH remarkably reduced enzyme productivity. In addition, a higher initial concentration of soybean flour reduced the enzyme productivity of cells. The pectin-releasing activity was the largest and reached up to 2200–2400 U/ml, when the culture medium containing an initial soybean flour concentration of 40 g/l was autoclaved for 45–60 min without alkaline solubilization treatment.
Antisense silencing of the creA Gene in Aspergillus nidulans.
Bautista, L. F., Aleksenko, A., Hentzer, M., Santerre-Henriksen, A. & Nielsen, J. (2000). Applied and Environmental Microbiology, 66(10), 4579-4581.
Antisense expression of a portion of the gene encoding the major carbon catabolite repressor CREA in Aspergillus nidulans resulted in a substantial increase in the levels of glucose-repressible enzymes, both endogenous and heterologous, in the presence of glucose. The derepression effect was approximately one-half of that achieved in a null creA mutant. Unlike results for that mutant, however, growth parameters and colony morphology in the antisense transformants were not affected.
Arabinase gene expression in Aspergillus niger: indications for coordinated regulation.
Flipphi, M. J. A., Visser, J., van der Veen, P. & de Graaff, L. H. (1994). Microbiology, 140(10), 2673-2682.
Aspergillus niger secretes three glycosylated glycosyl hydrolases which are involved in degradation of the plant cell wall polysaccharide L-arabinan: α-L-arabinofuranosidases (ABF) A and B, and endo-1,5-α-L-arabinase (ABN) A. The nucleotide sequence of the previously cloned gene encoding ABF A (abfA) from A. niger was determined. The coding region contains seven introns. Mature ABF A comprises 603 amino acids with a molecular mass of 65.4 kDa as deduced from the nucleotide sequence. The secreted enzyme is N-glycosylated. The primary structures of the three A. niger arabinases characterized lack similarity. Regulation of arabinase expression upon induction by sugar beet pulp and by L-arabitol was studied as a function of time. This was done in wild-type A. niger as well as in transformants carrying multiple copies of either one of the ABF-encoding genes. Each arabinase gene responded differently upon a mycelial transfer to L-arabitol-containing medium. Extra copies of abfA or abfB led to a decreased expression level of ABN A, though the repression elicited by abfB is stronger and more persistent than that effected by abfA. Multiple copies of both abf genes influence expression of the other ABF similarly, but to a far less pronounced degree than they affect ABN A synthesis. Four putative promoter elements, shared by all three arabinase genes, could be involved in coordination of L-arabinan degradation by A. niger.
Recombinant expression and characterization of XynD from Bacillus subtilis subsp. subtilis ATCC 6051: a GH 43 arabinoxylan arabinofuranohydrolase.
Bourgois, T. M., Van Craeyveld, V., Van Campenhout, S., Courtin, C. M., Delcour, J. A., Robben, J. & Volckaert, G. (2007). Applied Microbiology and Biotechnology, 75(6), 1309-1317.
The complete genome sequence of Bacillus subtilis reveals that sequences encoding several hemicellulases are co-localised with a gene (xynD) encoding a putative family 43 glycoside hydrolase that has not yet been characterised. In this work, xynD has been isolated from genomic DNA of B. subtilis subsp. subtilis ATCC 6051 and cloned for cytoplasmatic expression in Escherichia coli. Recombinant XynD (rXynD) was purified using ion-exchange chromatography and gel permeation chromatography. The enzyme had a molecular mass of approximately 52 kDa, a p/above 9.0 and releases α-L-arabinose from arabinoxylo-oligosaccharides as well as arabinoxylan polymers with varying degree of substitution. Using para -nitrophenyl-α-L-arabinofuranoside as substrate, maximum activity was observed at pH 5.6 and 45°C. The enzyme retained its activity over a large pH range, while activity was lost after pre-incubation above 50°C. Gas–liquid chromatography and proton nuclear magnetic resonance spectrometry analysis indicated that rXynD specifically releases arabinofuranosyl groups from mono-substituted C-(O)-2 and C-(O)-3 xylopyranosyl residues on the xylan backbone. As rXynD did not display endoxylanase, xylosidase or arabinanase activity and was inactive on arabinan, we conclude that this enzyme is best described as an arabinoxylan arabinofuranohydrolase.