Genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of the thermophilic Caldicoprobacter algeriensis TH7C1T

Background

Omics approaches are widely applied in the field of biology for the discovery of potential CAZymes including whole genome sequencing. The aim of this study was to identify protein encoding genes including CAZymes in order to understand glycans-degrading machinery in the thermophilic Caldicoprobacter algeriensis TH7C1^T strain.

Results

Caldicoprobacter algeriensis TH7C1^T is a thermophilic anaerobic bacterium belonging to the Firmicutes phylum, which grows between the temperatures of 55 °C and 75 °C. Next generation sequencing using Illumina technology was performed on the C. algeriensis strain resulting in 45 contigs with an average GC content of 44.9% and a total length of 2,535,023 bp. Genome annotation reveals 2425 protein-coding genes with 97 ORFs coding CAZymes. Many glycoside hydrolases, carbohydrate esterases and glycosyltransferases genes were found linked to genes encoding oligosaccharide transporters and transcriptional regulators; suggesting that CAZyme encoding genes are organized in clusters involved in polysaccharides degradation and transport. In depth analysis of CAZomes content in C. algeriensis genome unveiled 33 CAZyme gene clusters uncovering new enzyme combinations targeting specific substrates.

Conclusions

This study is the first targeting CAZymes repertoire of C. algeriensis, it provides insight to the high potential of identified enzymes for plant biomass degradation and their biotechnological applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01818-0.

Zero forcing number of fuzzy graphs with application

We introduce and study forcing number for fuzzy graphs. Also, we compute zero forcing numbers for some classes of graphs and extend this concept to fuzzy graphs. In this regard we obtain upper bounds for zero forcing of some classes of fuzzy graphs. We will proceed to obtain a new algorithm to computing zero forcing set and finding a formula for zero forcing number, and by some examples we illustrate these notions. Finally, we introduce some applications of fuzzy zero forcing in medical treatments.

The optimized production, purification, characterization, and application in the bread making industry of three acid-stable alpha-amylases isoforms from a new isolated Bacillus subtilis strain US586

A new alpha-amylase-producing strain was assigned as Bacillus subtilis US586. The used statistical methodology indicated that amylase production was enhanced by 5.3 folds. The crude enzyme analysis proved the presence of three amylases isoforms Amy1, Amy2, and Amy3 called Amy586. The purified amylases had molecular masses of 48, 52, and 68 kDa with a total specific activity of 2,133 U/mg. Amy586 generated maltose, maltotriose, and maltopentaose as main final products after starch hydrolysis. It exhibited a large 4-6 optimal pH, a 60°C temperature activity, and a moderate thermostability. Amy586 displayed a high pH stability ranging from 3.5 to 6. The addition of Amy586 to weak wheat flour decreased its P/L ratio from 1.9 to 1.2 and increased its dough baking strength (W) from 138 × 10^-4 to 172 × 10^-4  J. Amy586 also improved the bread texture parameters by reducing its firmness and boosting the cohesion and elasticity values. PRACTICAL APPLICATIONS: Bacterial alpha-amylases with novel properties have been the major extent of recent research. In this paper, we managed to demonstrate that the addition of a purified amylolytic extract from the new isolated Bacillus subtilis strain US586 to weak local flour improves dough rheological proprieties and bread quality. Therefore, Amy586 can be considered as a bread making improver.

Aspergillus oryzae S2 AmyA amylase expression in Pichia pastoris: production, purification and novel properties

A synthetic cDNA-AmyA gene was cloned and successfully expressed in Pichia pastoris as a His-tagged enzyme under the methanol inducible AOX1 promoter. High level of extracellular amylase production of 72 U/mL was obtained after a 72 h induction by methanol. As expected, the recombinant strain produced only the AmyA isoform since the host is a protease deficient strain. Besides, the purified r-AmyA showed a molecular mass of 54 kDa, the same pH optimum equal to 5.6 but a higher thermoactivity of 60 °C against 50 °C for the native enzyme. Unlike AmyA which maintained 50% of its activity after a 10-min incubation at 60 °C, r-AmyA reached 45 min. The higher thermoactivity and thermostability could be related to the N-glycosylation. The r-AmyA activity was enhanced by 46% and 45% respectively in the presence of 4 mM Fe²⁺ and Mg²⁺ ions. This enzyme was more efficient in bread-making since such ions were reported to have a positive impact on the nutriment quality and the rheological characteristics of the wheat flour dough. The thermoactivity/thermostability as well as the iron and magnesium activations could also be ascribed to the presence of an additional C-terminal loop containing the His tag.

Polybenzimidazoles/Phosphoric Acid Solid Polymer Electrolytes: Mechanical and Electrical Properties

Poly (2,2'-(m-phenylene) 5,5'-bibenzimidazole), PBI and poly (2,5-benzimidazole), ABPBI, were cast into films and doped with phosphoric acid. Their mechanical properties were studied as a function of inherent viscosity and phosphoric acid content. The commercial PBI with an I. V. of 0.8 to 0.9 had relatively low elongation at break. It was fractionated; the higher the inherent viscosity the higher the modulus and elongation. At low phosphoric acid doping the modulus rose because a crystalline phase developed, and then dropped as more phosphoric acid was added. A second doping method produced films with high crystallinity and higher conductivity (0.02-.03 vs. 0.06-.08 S/cm) but poorer elongation than those made by doping a cast film in phosphoric acid. In order to get higher molecular weight films that could have better mechanical properties, we decided to polymerize 3,4-diaminobenzoic acid to ABPBI, an AB polymer for which I. V.'s of∼16 have been reported. After learning how to purify and polymerize the monomer, I. V.'s of 6–8 were easily obtained. Conductivities of the doped ABPBI films were as high as those of the best PBI films. With their high viscosities, the ABPBI films were much tougher and had better elongation than the doped PBI films.