Purification and characterization of a xylanase and an arabinofuranosidase from Bacillus polymyxa

Paenibacillus lentus sp. nov., a β-mannanolytic bacterium isolated from mixed soil samples in a selective enrichment using guar gum as the sole carbon source

A novel bacterial strain, CMG1240T, was isolated in 1988 from mixed soil samples collected from the United States and South America in a selective enrichment medium with guar gum as the sole carbon source. This microbial isolate showed β-mannanolytic activity to hydrolyse the galactomannans present in guar gum. Strain CMG1240T was aerobic, Gram-stain-variable, non-motile, rod-shaped and endospore-forming. It was further examined based on a combination of phenotypic, physiological and genetic characterization. On the basis of 16S rRNA gene sequence similarity, cellular lipid profile and fatty acid composition, strain CMG1240T was shown to belong unequivocally to the genus Paenibacillus . Quinone analysis showed that MK-7 was the only menaquinone detected. The main cell-wall sugar was xylose with trace amounts of mannose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unknown glycolipids, phospholipids, phosphoglycolipids and other lipids. The peptidoglycan structure was A1γ (meso-diaminopimelic acid-direct). The major fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content was 46 mol% as determined experimentally and by analysis of the genomic sequence. The 16S rRNA gene sequence of strain CMG1240T shared highest similarity with that of Paenibacillus fonticola ZLT (97.6 %) while all other tested Paenibacillus strains showed lower sequence similarities (≤95.3 %). The results of DNA–DNA hybridization and chemotaxonomic tests enabled the genotypic and phenotypic differentiation of strain CMG1240T from P. fonticola . Based on these results, strain CMG1240T ( = ATCC BAA-2594T = DSM 25539T) should be designated the type strain of a novel species within the genus Paenibacillus , for which the name Paenibacillus lentus sp. nov. is proposed.

Paenibacillus sacheonensis sp. nov., a xylanolytic and cellulolytic bacterium isolated from tidal flat sediment

A Gram-negative-staining, rod-shaped bacterium, designated strain SY01T, was isolated from tidal flat sediment from Sacheon Bay, South Korea. Strain SY01T was characterized with respect to its phenotypic and phylogenetic characteristics. The novel strain was spore-forming, motile, catalase-negative and oxidase-positive. Optimal growth of the strain occurred at 30 °C and pH 7.0. The DNA G+C content was 56.1 mol%. The predominant menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids were detected in the polar lipid profile. Anteiso-C15 : 0 (47.2 %), iso-C15 : 0 (18.9 %) and iso-C16 : 0 (10.5 %) were the major cellular fatty acids of strain SY01T. The highest 16S rRNA gene sequence similarities were found with Paenibacillus phyllosphaerae PALXIL04T (95.9 %), Paenibacillus tarimensis SA-7-6T (94.6 %) and Paenibacillus mendelii C/2T (94.4 %). Based on the phylogenetic, chemotaxonomic and physiological characteristics presented in this study, strain SY01T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus sacheonensis sp. nov. is proposed. The type strain is SY01T ( = DSM 23054T = KACC 14895T).

Paenibacillus xylanisolvens sp. nov., a xylan-degrading bacterium from soil

A xylan-degrading bacterium, strain X11-1T, was isolated from soil collected in Nan province, Thailand. The strain was characterized based on its phenotypic and genotypic characteristics. Strain X11-1T was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7, anteiso-C15 : 0 (56.6 %) and C16 : 0 (14.0 %) were the predominant cellular fatty acids and diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol were the major phospholipids. The DNA G+C content was 51.6 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain X11-1T was affiliated to the genus Paenibacillus and was closely related to Paenibacillus naphthalenovorans KACC 11505T and Paenibacillus validus CCM 3894T, with 96.5 % sequence similarity. Therefore, the strain represents a novel species of the genus Paenibacillus, for which the name Paenibacillus xylanisolvens sp. nov. is proposed. The type strain is X11-1T (=KCTC 13042T =PCU 311T =TISTR 1829T).

Paenibacillus cellulosilyticus sp. nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera

A bacterial strain designated PALXIL08(T) was isolated from the phyllosphere of Phoenix dactylifera bracts. A phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate within the genus Paenibacillus in the same subgroup as Paenibacillus kobensis and Paenibacillus curdlanolyticus (98.9 and 97.9 % sequence similarity, respectively). The DNA hybridization values between the isolate and the type strains of Paenibacillus kobensis and Paenibacillus curdlanolyticus were found to be 27.4 and 17.6 %, respectively. The isolate comprised Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced and cellulose, xylan, starch and aesculin were hydrolysed. Many carbohydrates served as carbon sources for growth. MK-7 was the predominant menaquinone, and anteiso-C(15 : 0) and iso-C(16 : 0) were the major fatty acids. The DNA G+C content was 51 mol%. DNA relatedness data and the results of phylogenetic and phenotypic analyses showed that strain PALXIL08(T) should be considered as the type strain of a novel species of the genus Paenibacillus, for which the name Paenibacillus cellulosilyticus sp. nov. is proposed. The type strain is PALXIL08(T) (=LMG 22232(T)=CECT 5696(T)).

Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from the phyllosphere of Phoenix dactylifera

A bacterial strain, designated PALXIL04T, was isolated from the phyllosphere of Phoenix dactylifera. Phylogenetic analysis placed the isolate within the genus Paenibacillus with the closest relatives being Paenibacillus curdlanolyticus and Paenibacillus kobensis. DNA–DNA hybridization measurements showed low DNA relatedness (15–20 %) between the isolate and its closest relatives. Cells were Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced by the organism. Cellulose, starch, aesculin and xylan were hydrolysed. Growth was supported by many carbohydrates as the carbon source. MK-7 was the predominant menaquinone and anteiso-C15 : 0 the major fatty acid. The G+C content of the DNA was 50·7 mol%. Phylogenetic, DNA–DNA relatedness and phenotypic analyses indicated that strain PALXIL04T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus phyllosphaerae sp. nov. is proposed. The type strain is PALXIL04T (=LMG 22192T=CECT 5862T).

Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium

During a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99·3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA–DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content of strain XIL14T was 50·5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and β-galactosidase. DNA–DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43·3 and 36·3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T).

Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces

During a search for xylan-degrading micro-organisms, a sporulated bacterium was recovered from recent and old cow dung and rectal samples. The isolates were identified as members of a novel species of the genus Paenibacillus, based on 16S rRNA gene sequences. According to the results of phylogenetic analysis, the most closely related species was Paenibacillus azoreducens. Phenotypic and chemotaxonomic analyses and DNA–DNA hybridization experiments also showed that the isolates belonged to a novel species of the genus Paenibacillus. The novel species is a facultatively anaerobic, motile, Gram-variable, sporulated rod. The spores of this rod-shaped micro-organism occur in slightly swollen sporangia and are honeycomb-shaped. The main fatty acid is anteiso-branched C15 : 0. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. The novel species produces a wide variety of hydrolytic enzymes, such as xylanases, cellulases, amylases, gelatinase, urease and β-galactosidase. On the contrary, it does not produce caseinase, phenylalanine deaminase or lysine decarboxylase. According to the data obtained in this work, the strains belong to a novel species, for which the name Paenibacillus favisporus sp. nov. is proposed (type strain, GMP01T=LMG 20987T=CECT 5760T).

Purification and partial characterization of alpha-L-arabinofuranosidase produced by Thermomonospora fusca

Thermomonospora fusca produced a relatively high level of alpha-L-arabinofuranosidase when growing on oat spelt xylan as the main carbon and energy source. The enzyme exhibited maximum relative activity (0.136 U/g protein) at pH 9.0 with 54 and 55% activity remaining at pH of 4.5 and 11.0, respectively. The apparent Km value for the crude alpha-L-arabinofuranosidase preparation was 180 mumol/L 4-nitrophenyl alpha-L-arabinofuranoside; the upsilon lim value was the release of 40 mumol/L 4-nitrophenol per min. Enzyme activity was eluted as a single peak (HPLC gel filtration chromatography) corresponding to molar mass of approximately 92 kDa. Native electrophoresis of crude cell lysate confirmed the presence of a single active intracellular alpha-L-arabinofuranosidase component. SDS-PAGE of this enzyme, developed as zymogram, did not demonstrate any activity; denaturing gel was stained and a protein band of relative molar mass of 46 kDa was revealed. Isoelectric focusing of a purified alpha-L-arabinofuranosidase yielded a single protein band for the corresponding activity zone with pI 7.9. The enzyme was purified approximately 21-fold the mean overall yield was about 16%.

α-l-Arabinofuranosidases

Interest in the alpha-L-arabinofuranosidases has increased in recent years because of their application in the conversion of various hemicellulosic substrates to fermentable sugars for subsequent production of fuel alcohol. Xylanases, in conjunction with alpha-L-arabinofuranosidases and other accessory enzymes, act synergistically to degrade xylan to component sugars. The induction of alpha-L-arabinofuranosidase production, physico-chemical characteristics, substrate specificity, and molecular biology of the enzyme are described. The current state of research and development of the arabinofuranosidases and their role in biotechnology are presented.

Purification and characterization of a moderately thermostable xylanase from Bacillus sp. strain SPS-0

A Bacillus spp. strain SPS-0, isolated from a hot spring in Portugal, produced an extracellular xylanase upon growth on wheat bran arabinoxylan. The enzyme was purified to homogeneity by ammonium sulfate precipitation, anion exchange, gel filtration, and affinity chromatography. The optimum temperature and pH for activity was 75 degrees C and 6.0. Xylanase was stable up to 70 degrees C for 4 h at pH 6.0 in the presence of xylane. Xylanase was completely inhibited by the Hg(2+) ions. beta-Mercaptoethanol, dithiothreitol, and Mn(2+) stimulated the xylanase activity. The products of birchwood xylan hydrolysis were xylose, xylobiose, xylotriose, and xylotetraose. Kinetic experiments at 60 degrees C and pH 6.0 gave V(max) and K(m)values of 2420 nkat/mg and 0.7 mg/ml.

Xylanolytic enzymes from fungi and bacteria

The development of new analytical techniques and the commercial availability of new substrates have led to the purification and characterization of a large number of xylan-degrading enzymes. Furthermore, the introduction of recombinant DNA technology has resulted in the selection of xylanolytic enzymes that are more suitable for industrial applications. For a successful integration of xylanases in industrial processes, a detailed understanding of the mechanism of enzyme action is, however, required. This review gives an overview of various xylanolytic enzyme systems from bacteria and fungi that have been described recently in more detail.

Purification and characterization of an arabinofuranosidase from Bacillus polymyxa expressed in Bacillus subtilis

Two polypeptides showing alpha-L-arabinofuranosidase activity have been purified to homogeneity from culture supernatants of a Bacillus subtilis clone harbouring the xynD gene [Gosalbes et al. (1991) J Bacteriol 173: 7705-7710] from Bacillus polymyxa. Both polypeptides, with determined molecular masses of 64 kDa and 53 kDa, share the same sequence at their N termini, which also coincides with the sequence deduced for the mature protein from the previously determined sequence of nucleotides (Gosalbes et al. 1991). The two polypeptides have been biochemically characterized. Arabinose is the unique product released from arabinose-containing xylans which are substrates for both enzyme forms. Other natural arabinose-containing polysaccharides, such as arabinogalactans, are not attacked by them but some artificial arabinose derivatives are good substrates for both polypeptides. Their arabinose-releasing activity on arabinoxylans facilitates the hydrolysis of the xylan backbone by some endoxylanases from Bacillus polymyxa.