Purification and properties of an enzyme capable of degrading the sheath of Sphaerotilus natans

Antimicrobial high molecular weight pectin polysaccharides production from diverse citrus peels using a novel PL10 family pectate lyase

The discovery of environmentally friendly enzymes that can convert inexpensive and abundant citrus peel pectin into high value-added product is a potential avenue for the citrus peel application. In this study, a novel PL10-family pectate lyase (pelA) was characterized from marine bacterium Echinicola pacifica. PelA was a Ca²⁺ dependent pectate lyase whose activity was highest at pH 8 and 40 °C. It was capable of degrading polygalacturonic acid (PGA) and citrus peel pectin (CPP), but not apple peel pectin. Notably, PelA hydrolyzed PGA to high molecular weight polysaccharide (average molecular weight 111.4 kDa). Moreover, PelA was also able to degrade CPP from nine distinct citrus species into polysaccharides (average molecular weight ranging from 84.7 to 539.2 kDa) that showed antimicrobial activity against Staphylococcus epidermidis (88.8 %), Bacillus subtilis (99.8 %), Staphylococcus aureus (92.1 %), Escherichia coli (100.0 %) and Klebsiella pneumoniae (86.4 %). Considering the high market value of pectin in the food industry, PelA's capacity to convert citrus pectin into high molecular weight polysaccharides lays a foundation for its applications.

Structural determination of the sheath-forming polysaccharide of Sphaerotilus montanus using thiopeptidoglycan lyase which recognizes the 1,4 linkage between α-d-GalN and β-d-GlcA

Sphaerotilus natans is a filamentous sheath-forming bacterium commonly found in activated sludge. Its sheath is assembled from a thiolic glycoconjugate called thiopeptidoglycan. S. montanus ATCC-BAA-2725 is a sheath-forming member of stream biofilms, and its sheath is morphologically similar to that of S. natans. However, it exhibits heat susceptibility, which distinguishes it from the S. natans sheath. In this study, chemical composition and solid-state NMR analyses suggest that the S. montanus sheath is free of cysteine, indicating that disulfide linkage is not mandatory for sheath formation. The S. montanus sheath was successfully solubilized by N-acetylation, allowing solution-state NMR analysis to determine the sugar sequence. The sheath was susceptible to thiopeptidoglycan lyase prepared from the thiopeptidoglycan-assimilating bacterium, Paenibacillus koleovorans. The reducing ends of the enzymatic digests were labeled with 4-aminobenzoic acid ethyl ester, followed by HPLC. Two derivatives were detected, and their structures were determined. We found that the sheath has no peptides and is assembled as follows: [→4)-β-d-GlcA-(1→4)-β-d-Glc-(1→3)-β-d-GalNAc-(1→4)-α-d-GalNAc-(1→4)-α-d-GalN-(1→]_n (β-d-Glc and α-d-GalNAc are stoichiometrically and substoichiometrically 3-O-acetylated, respectively). Thiopeptidoglycan lyase was thus confirmed to cleave the 1,4 linkage between α-d-GalN and β-d-GlcA, regardless of the peptide moiety. Furthermore, vital fluorescent staining of the sheath demonstrated that elongation takes place at the tips, as with the S. natans sheath.

A novel thermostable α-1,3-glucanase from Streptomyces thermodiastaticus HF 3-3

Thermally stable α-1,3-glucanase HF65 was purified from culture filtrate of Streptomyces thermodiastaticus HF3-3. The molecular mass of this enzyme was estimated to be 65 kDa and 45.7 kDa by using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and size exclusion chromatography, respectively. The purified enzyme retained more than 50% of maximum activity even after incubation at 65°C more than 2 h. Moreover, α-1,3-glucanase HF65 was stable in the presence of chemicals like SDS, benzethonium chloride, and sodium fluoride at a concentration of 1%. The enzyme also exhibited salt tolerance at a concentration up to 20%. The observed stability of α-1,3-glucanase HF65 to salt and surfactants is a great advantage for its addition to commercial oral care products. Interestingly, the N-terminal amino acid sequence did not show any similarity to those of known α-1,3-glucanases, while the sequence of internal eight amino acid residues of this enzyme was homologous with those of mycodextranases. Nevertheless, the enzyme exhibited high specificity against α-1,3-glucan. According to these results, the enzyme purified from S. thermodiastaticus HF3-3 was classified as α-1,3-glucanase which was highly homologous to mycodextranase in amino acid sequence.

Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT

The marine flavobacterium Zobellia galactanivorans Dsij^T was isolated from a red alga and by now constitutes a model for studying algal polysaccharide bioconversions. We present an in-depth analysis of its complete genome and link it to physiological traits. Z. galactanivorans exhibited the highest gene numbers for glycoside hydrolases, polysaccharide lyases and carbohydrate esterases and the second highest sulfatase gene number in a comparison to 125 other marine heterotrophic bacteria (MHB) genomes. Its genome contains 50 polysaccharide utilization loci, 22 of which contain sulfatase genes. Catabolic profiling confirmed a pronounced capacity for using algal polysaccharides and degradation of most polysaccharides could be linked to dedicated genes. Physiological and biochemical tests revealed that Z. galactanivorans stores and recycles glycogen, despite loss of several classic glycogen-related genes. Similar gene losses were observed in most Flavobacteriia, suggesting presence of an atypical glycogen metabolism in this class. Z. galactanivorans features numerous adaptive traits for algae-associated life, such as consumption of seaweed exudates, iodine metabolism and methylotrophy, indicating that this bacterium is well equipped to form profitable, stable interactions with macroalgae. Finally, using statistical and clustering analyses of the MHB genomes we show that their carbohydrate catabolism correlates with both taxonomy and habitat.

Structural analysis of the sheath of a sheathed bacterium, Leptothrix cholodnii

Leptothrix cholodnii is an aerobic sheath-forming bacterium often found in oligotrophic and metal-rich aquatic environments. The sheath of this bacterium was isolated by selectively lysing the cells. Glycine and cysteine were the major amino acids of the sheath. The sheath was readily dissolved in hydrazine, and a polysaccharide substituted with cysteine was recovered from the solution. Galactosamine, glucosamine and galacturonic acid were detected in the hydrazinolysate by gas liquid chromatography analysis. FAB-MS analysis of the hydrazinolysate suggested a sugar sequence of HexN-GalA-HexN-HexN. Methylation linkage analysis revealed the presence of 4-linked GalA, 3-linked HexN and 4-linked HexN. The sulfhydryl groups of the sheath were used for labeling with the fluorogenic reagent, 4-(aminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (ABD-F). The labeled sheath (ABD-sheath) was partially hydrolyzed and three fluorescent fragments were purified by HPLC. One of them was identified as ABD-cysteine. The second one was found to be the ABD-cysteine tetramer. Another fragment was indicated to be a pentasaccharide substituted with ABD-cysteine by nuclear magnetic resonance (NMR) analysis. It can be assumed that the polysaccharide and peptide moieties of the sheath are connected by a cysteine residue. NMR analysis of the hydrazinolysate revealed that the polysaccharide moiety of the sheath was constructed from a pentasaccharide repeating unit containing 2-amino-2-deoxygalacturonic acid (GalNA), as shown below. -->4)-alpha-GalNA-(1-->4)-alpha-D-GalN(p)-(1-->4)-alpha-D-GalA(p)-(1-->4)-beta-D-GlcN(p)-(1-->3)-beta-D-GalN(p)-(1-->.

Degradation of rice bran hemicellulose by Paenibacillus sp. strain HC1: gene cloning, characterization and function of β-D-glucosidase as an enzyme involved in degradation

A bacterium (strain HC1) capable of assimilating rice bran hemicellulose was isolated from a soil and identified as belonging to the genus Paenibacillus through taxonomical and 16S rDNA sequence analysis. Strain HC1 cells grown on rice bran hemicellulose as a sole carbon source inducibly produced extracellular xylanase and intracellular glycosidases such as beta-D-glucosidase and beta-D-arabinosidase. One of them, beta-D-glucosidase, was further analyzed. A genomic DNA library of the bacterium was constructed in Escherichia coli and gene coding for beta-D-glucosidase was cloned by screening for beta-D-glucoside-degrading phenotype in E. coli cells. Nucleotide sequence determination indicated that the gene for the enzyme contained an open reading frame consisting of 1,347 bp coding for a polypeptide with a molecular mass of 51.4 kDa. The polypeptide exhibits significant homology with other bacterial beta-D-glucosidases and belongs to glycoside hydrolase family 1. Beta-D-Glucosidase purified from E. coli cells was a monomeric enzyme with a molecular mass of 50 kDa most active at around pH 7.0 and 37 degrees C. Strain HC1 glycosidases responsible for degradation of rice bran hemicellulose are expected to be useful for structurally determining and molecularly modifying rice bran hemicellulose and its derivatives.

Paenibacillus hodogayensis sp. nov., capable of degrading the polysaccharide produced by Sphaerotilus natans

Sphaerotilus natans is a sheathed bacterium often found in activated sludge that has a bulking problem. A bacterial strain that is able to degrade the extracellular polysaccharide produced by S. natans was isolated. The isolate was a spore-forming, aerobic, rod-shaped bacterium. The Gram reaction was variable or negative. The optimum growth temperature was 30 degrees C and the optimum pH was 8. The G+C content of the DNA was 55 mol%. The major cellular fatty acid and respiratory quinone were anteiso-C(15 : 0) and MK-7, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolate was a member of the genus Paenibacillus. The nearest relative, with a similarity of 94.2 %, was Paenibacillus koleovorans, a bacterium capable of degrading the sheath of S. natans. The phenotypic characteristics of the isolate were apparently different from those of related species in the genus Paenibacillus. It is proposed that the isolate be designated Paenibacillus hodogayensis sp. nov. The type strain is SG(T) (=JCM 12520(T)=KCTC 3919(T)).

Structure of the polysaccharide isolated from the sheath of Sphaerotilus natans

A polysaccharide was isolated from the sheath of a sheathed bacterium, Sphaerotilus natans. The sheath polysaccharide (SPS) was composed of D-glucose and D-(N-acetyl)galactosamine in molar ratios of 1:4. Methylation linkage analysis revealed the presence of the residues of 4-linked glucose, 4-linked (N-acetyl)galactosamine, and 3-linked (N-acetyl)galactosamine in molar ratios of 1:3:1. The oligomer of SPS was prepared with an SPS-specific degrading enzyme from a sheath-degrading bacterium, Paenibacillus koleovorans. The oligomer was derivatized and subjected to fast atom bombardment-mass spectrometry to investigate the monosaccharide sequence of SPS. The structure of SPS was confirmed by nuclear magnetic resonance. The resulting data showed that SPS is a straight-chained basic polysaccharide constructed of a pentasaccharide repeating unit.

Identification of a gene essential for sheathed structure formation in Sphaerotilus natans, a filamentous sheathed bacterium

Sphaerotilus natans, a filamentous bacterium that causes bulking in activated sludge processes, can assume two distinct morphologies, depending on the substrate concentration for growth; in substrate-rich media it grows as single rod-shaped cells, whereas in substrate-limited media it grows as filaments. To identify genes responsible for sheath formation, we carried out transposon Tn5 mutagenesis. Of the approximately 20,000 mutants obtained, 7 did not form sheathed structures. Sequencing of the Tn5-flanking regions showed that five of the seven Tn5 insertions converged at the same open reading frame, designated sthA. The deduced amino acids encoded by sthA were found to be homologous to glycosyltransferase, which is known to be involved in linking sugars to lipid carriers during bacterial exopolysaccharide biosynthesis. Disruption of the gene of the wild-type strain by inserting a kanamycin resistance gene cassette also resulted in sheathless growth under either type of nutrient condition. These findings indicate that sthA is a crucial component responsible for sheath formation.