A simple assay procedure for beta-D-mannanase

Multi-Omics Characterization of Host-Derived Bacillus spp. Probiotics for Improved Growth Performance in Poultry

Microbial feed ingredients or probiotics have been used widely in the poultry industry to improve production efficiency. Spore-forming Bacillus spp. offer advantages over traditional probiotic strains as Bacillus spores are resilient to high temperature, acidic pH, and desiccation. This results in increased strain viability during manufacturing and feed-pelleting processes, extended product shelf-life, and increased stability within the animal’s gastrointestinal tract. Despite numerous reports on the use of Bacillus spores as feed additives, detailed characterizations of Bacillus probiotic strains are typically not published. Insufficient characterizations can lead to misidentification of probiotic strains in product labels, and the potential application of strains carrying virulence factors, toxins, antibiotic resistance, or toxic metabolites. Hence, it is critical to characterize in detail the genomic and phenotypic properties of these strains to screen out undesirable properties and to tie individual traits to clinical outcomes and possible mechanisms. Here, we report a screening workflow and comprehensive multi-omics characterization of Bacillus spp. for use in broiler chickens. Host-derived Bacillus strains were isolated and screened for desirable probiotic properties. The phenotypic, genomic and metabolomic analyses of three probiotic candidates, two Bacillus amyloliquefaciens (Ba ATCC PTA126784 and ATCC PTA126785), and a Bacillus subtilis (Bs ATCC PTA126786), showed that all three strains had promising probiotic traits and safety profiles. Inclusion of Ba ATCC PTA12684 (Ba-PTA84) in the feed of broiler chickens resulted in improved growth performance, as shown by a significantly improved feed conversion ratio (3.3%), increased of European Broiler Index (6.2%), and increased average daily gain (ADG) (3.5%). Comparison of the cecal microbiomes from Ba PTA84-treated and control animals suggested minimal differences in microbiome structure, indicating that the observed growth promotion presumably was not mediated by modulation of cecal microbiome.

Expression and Characterization of the RKOD DNA Polymerase in Pichia pastoris

The present study assessed high-level expression of the KOD DNA polymerase in Pichia pastoris. Thermococcus kodakaraensis KOD1 is a DNA polymerase that is widely used in PCR. The DNA coding sequence of KOD was optimized based on the codon usage bias of P. pastoris and synthesized by overlapping PCR, and the nonspecific DNA-binding protein Sso7d from the crenarchaeon Sulfolobus solfataricus was fused to the C-terminus of KOD. The resulting novel gene was cloned into a pHBM905A vector and introduced into P. pastoris GS115 for secretory expression. The yield of the target protein reached approximately 250 mg/l after a 6-d induction with 1% (v/v) methanol in shake flasks. This yield is much higher than those of other DNA polymerases expressed heterologously in Escherichia coli. The recombinant enzyme was purified, and its enzymatic features were studied. Its specific activity was 19,384 U/mg. The recombinant KOD expressed in P. pastoris exhibited excellent thermostability, extension rate and fidelity. Thus, this report provides a simple, efficient and economic approach to realize the production of a high-performance thermostable DNA polymerase on a large scale. This is the first report of the expression in yeast of a DNA polymerase for use in PCR.

Redesign the α/β fold to enhance the stability of mannanase Man23 from Bacillus subtilis

In this work, we engineered the α/β fold of mannanase Man23 based on its molecular structure analysis to obtain more stable variants. By introducing 31 single-site mutations in the α/β fold and shuffling them, the incorporation of four mutations (K178R, K207R, N340R, and S354R) displayed a good balance between high activity and stability at higher temperature and broader pH. This quartet variant was characterized by an almost threefold increased activity and a sevenfold increased stability compared to native mannanase Man23. Our results suggest that such work is safe to increase our target protein stability with no loss of activity.

Transcriptional regulation and molecular characterization of the manA gene encoding the biofilm dispersing enzyme mannan endo-1,4-beta-mannosidase in Xanthomonas campestris

Exopolysaccharide and several extracellular enzymes of Xanthomonas campestris pv. campestris (Xcc), the causative agent of black rot in crucifers, are important virulence determinants. It is known that Clp (cAMP receptor protein-like protein) and RpfF (an enoyl-CoA hydratase homologue required for the synthesis of diffusible signal factor, DSF) regulate the production of these determinants. Addition of DSF or Xcc extracellular protein containing partially purified mannanase (EC 3.2.1.78, encoded by manA) can disperse the cell aggregates formed by rpfF mutant. In this study, nucleotide G 64 nt upstream of the manA translation start codon was determined as the transcription initiation site by the 5' RACE technique. Transcriptional fusion assays showed that manA transcription is positively regulated by Clp and RpfF and induced by locust bean gum. The manA coding region was cloned and expressed in E. coli as recombinant ManA (rManA). The rManA was purified by affinity chromatography, and its biochemical properties were characterized. The rManA had a pH optimum at 7.0 (0.1 M Hepes) and a temperature optimum at about 37 degrees C. Sequence and mutational analyses demonstrated that Xcc manA encodes the major mannanase, a member of family 5 of glycosyl hydrolases. This study not only extends previous work on Clp and RpfF regulation by showing that they both influence the expression of manA in Xcc, but it also for the first time characterizes Xanthomonas mannanase at the protein level.

Preparation of a new chromogenic substrate to assay for beta-galactanases that hydrolyse type II arabino-3,6-galactans

A chromogenic assay using RB5-dGA, Reactive Black 5 (RB5) dye covalently coupled to de-arabinosylated gum arabic (dGA), was developed for rapid screening of beta-galactanases. dGA was prepared by partial acid hydrolysis (0.25M trifluoroacetic acid for 2h at 90-95 degrees C) of gum Arabic (GA) from Acacia senegal. The dGA exhibited a median molecular mass of approximately 10kDa, corresponding to a degree of polymerisation (DP) approximately 60. It was devoid of Ara residues, and contained mostly Galp (68mol%) together with GlcpA (30mol%). The Galp residues were (1,6)- (34mol%), (1,3)- (3mol%) and (1,3,6)- (26mol%) linked, and the GlcAp residues were primarily terminal (28mol%) together with a small amount of (1,4)-linked (2mol%), as expected for a type II (3,6)-galactan. The new chromogenic assay is simple, cost effective, relatively sensitive, and is specific for either beta-(1-->3)- and/or beta-(1-->6)-d-galactanases. It will enable routine large-scale screening of beta-galactanases from crude enzyme preparations and microorganism cultures, and is suitable for profiling activity during purification processes.

Gel diffusion assays for endo-beta-mannanase and pectin methylesterase can underestimate enzyme activity due to proteolytic degradation: a remedy

The accuracy of the sensitive gel-diffusion assay for endo-beta-mannanase activity was improved when protein was added to fruit extracts or into the substrate-gel matrix in which the enzyme assays were conducted. Mixing of commercially available protease inhibitors with fruit enzyme extracts also resulted in increased assayable activity. These treatments were less effective when applied to extracts from tomato seeds, which contained over three times more endogenous protein than fruit extracts. Thus the presence of added or higher amounts of endogenous proteins served as the protectant for endo-beta-mannanase during the course of the gel-diffusion assay, which required an incubation at 32 degrees C for at least 18 h. There was no difference in assayable endo-beta-mannanase activity in the presence and absence of added protein when measured rapidly by viscometry. An effective modification was made to the galactomannan substrate gel assay for endo-beta-mannanase, which is the most efficient method for assaying large numbers of extracts, to improve its accuracy when the enzyme is obtained from tissues containing a low endogenous protein content. This involved incorporating an optimal concentration of gelatin into the galactomannan assay matrix gel. Much higher enzyme activities were recorded, with up to a 10-fold increase for tomato fruit extracts, compared to the same samples assayed on gels with no gelatin added. This increased activity was also obtained using extracts from the fruit of cantaloupe, peach, and nectarine. When incorporated into esterified pectin substrate gels, gelatin also increased the assayable activity of pectin methylesterase. Thus the incorporation of protein (gelatin) into substrate gels during the assay also should be widely more useful for other cell-wall-mobilizing enzymes and hydrolases.

Galactomannanases Man2 and Man5 from Thermotoga species: growth physiology on galactomannans, gene sequence analysis, and biochemical properties of recombinant enzymes

The enzymatic hydrolysis of mannan-based hemicelluloses is technologically important for applications ranging from pulp and paper processing to food processing to gas and oil well stimulation. In many cases, thermostability and activity at elevated temperatures can be advantageous. To this end, the genes encoding beta-mannosidase (man2) and beta-mannanase (man5) from the hyperthermophilic bacteria Thermotoga neapolitana 5068 and Thermotoga maritima were isolated, cloned, and expressed in Escherichia coli. The amino acid sequences for the mannosidases from these organisms were 77% identical and corresponded to proteins with an M(r) of approximately 92 kDa. The translated nucleotide sequences for the beta-mannanase genes (man5) encoded polypeptides with an M(r) of 76 kDa that exhibited 84% amino acid sequence identity. The recombinant versions of Man2 and Man5 had similar respective biochemical and biophysical properties, which were also comparable to those determined for the native versions of these enzymes in T. neapolitana. The optimal temperature and pH for the recombinant Man2 and Man5 from both organisms were approximately 90 degrees C and 7.0, respectively. The presence of Man2 and Man5 in these two Thermotoga species indicates that galactomannan is a potential growth substrate. This was supported by the fact that beta-mannanase and beta-mannosidase activities were significantly stimulated when T. neapolitana was grown on guar or carob galactomannan. Maximum cell densities increased by at least tenfold when either guar or carob galactomannan was added to the growth medium. For T. neapolitana grown on guar at 83 degrees C, Man5 was secreted into the culture media, whereas Man2 was intracellular. These localizations were consistent with the presence and lack of signal peptides for Man5 and Man2, respectively. The identification of the galactomannan-degrading enzymes in these Thermotoga species adds to the list of biotechnologically important hemicellulases produced by members of this hyperthermophilic genera.

Purification and characterization of extremely thermostable beta-mannanase, beta-mannosidase, and alpha-galactosidase from the hyperthermophilic eubacterium Thermotoga neapolitana 5068

Thermostable and thermoactive beta-mannanase (1,4-beta-D-mannan mannanohydrolase [EC 3.2.1.78]), beta-mannosidase (beta-D-mannopyranoside hydrolase [EC 3.2.1.25]) and alpha-galactosidase (alpha-D-galactoside galactohydrolase [EC 3.2.1.22]) were purified to homogeneity from cell extracts and extracellular culture supernatants of the hyperthermophilic eubacterium Thermotoga neapolitana 5068 grown on guar gum-based media. The beta-mannanase was an extracellular monomeric enzyme with a molecular mass of 65 kDa. The optimal temperature for activity was 90 to 92 degrees C, with half-lives (t1/2) of 34 h at 85 degrees C, 13 h at 90 degrees C, and 35 min at 100 degrees C. The beta-mannosidase and alpha-galactosidase were found primarily in cell extracts. The beta-mannosidase was a homodimer consisting of approximately 100-kDa molecular mass subunits. The optimal temperature for activity was 87 degrees C, with t1/2 of 18 h at 85 degrees C, 42 min at 90 degrees C, and 2 min at 98 degrees C. The alpha-galactosidase was a 61-kDa monomeric enzyme with a temperature optimum of 100 to 103 degrees C and t1/2 of 9 h at 85 degrees C, 2 h at 90 degrees C, and 3 min at 100 degrees C. These enzymes represent the most thermostable and thermoactive versions of these types yet reported and probably act synergistically to hydrolyze extracellular galactomannans to monosaccharides by T. neapolitana for nutritional purposes. The significance of such substrates in geothermal environments remains to be seen.

Soluble chromogenic substrates for the assay of endo-1,4-beta-xylanases and endo-1,4-beta-glucanases

New soluble chromogenic substrates were prepared for specific and rapid assays of endo-1,4-beta-xylanases and endo-1,4-beta-glucanases. A soluble beechwood 4-O-methyl-D-glucurono-D-xylan was dyed with Remazol brilliant blue R, and hydroxyethylcellulose was coupled to Ostazin brilliant red H-3B. The assays are based on photometric measurements of the enzyme-released dyed fragments soluble in the presence of organic solvents which precipitate the original substrates and their high-molecular-weight fractions. The assays are advantageous for rapid analyses of large amount of samples and also permit evaluation of the activities of both enzymes in the presence of exo-beta-glycanases and beta-glycosidases, at a high level of reducing compounds and viable cells, on the cell surface and on cell membranes and organelles.

New chromogenic substrates for the assay of alpha-amylase and (1 leads to 4)-beta-D-glucanase

New chromogenic substrates have been developed for the quantitative assay of alpha-amylase and (1 leads to 4)-beta-D-glucanase. These were prepared by chemically modifying amylose or cellulose before dyeing, to increase solubility. After dyeing, the substrates were either soluble or could be readily dispersed to form fine, gelatinous suspensions. Assays based on the use of these substrates are sensitive and highly specific for either alpha-amylase or (1 leads to 4)-beta-D-glucanase. The method of preparation can also be applied to obtain substrates for other endo-hydrolases.

Beta-D-mannanases in germinating lucerne (alfalfa) seeds

Extraction and fractionation of the beta-D-mannanases in germinating lucerne produced four fractions if extracts were stored prior to chromatography. However, when extracts were applied rapidly to DEAE-cellulose, one of the fractions of high molecular weight (separated subsequently by gel chromatography) was not detected, indicating that it was formed after maceration. On storage, the amount of the lower-molecular-weight, unbound fraction from chromatography on DEAE-cellulose did not increase relative to that bound. During germination, the bound and unbound fractions both increased initially and then decreased, with only small changes in the ratio of each. The results suggest that three of the beta-D-mannanase fractions are formed in vivo prior to maceration.