3-(5-(1H-imidazol-1-yl) pent-1-en-1-yl)-9-ethyl-9H-carbazole: synthesis, characterization (IR, NMR), DFT, antimicrobial-antioxidant activities and docking study.

3-(5-(1H-imidazol-1-yl) pent-1-en-1-yl)-9-ethyl-9H-carbazole called as compound 1 was synthesized and characterized by proton and carbon-13 nuclear magnetic resonance (1H- and 13C- NMR) and Fourier transform infrared (FTIR) spectroscopic methods. Density Functional Theory/Becke, 3-parameter (DFT/B3LYP), for compound 1 were performed with 6-311++G(d,p) method. Optimized geometry, frontier molecular orbitals (HOMO; highest occupied molecular orbital; LUMO: lowest unoccupied molecular orbital), IR and NMR parameters of compound 1 were obtained. The evaluations reveal that the calculation results support the experimental results. In addition, the antimicrobial (a microwell dilution method) and antioxidant activities (2,2-Diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) ferric ion reducing antioxidant power (FRAP) of compound 1 were evaluated. According to the results obtained, it showed higher antimicrobial activity (Minimal inhibition concentration (MIC): 78.12 µg/mL) against B. subtilis subsp. Spizizenii. Morever, molecular docking studies were carried out to investigate the interactions of an antimicrobial agent on some important enzymes played important roles in nucleic acid (Deoxyribo nucleic acid (DNA) synthesis, cell wall synthesis, protein synthesis, and metabolism etc. The compound 1 was strongly bound to tyrosyl-tRNA synthetase enzyme (binding energy: -11.18 and Ki: 6.37 nM) and Beta-Ketoacyl-Acp Synthase III enzyme (binding energy: -10.29 and Ki: 28.47 nM).Communicated by Ramaswamy H. Sarma.

Cloning, biochemical characterization and molecular docking of novel thermostable ß-glucosidase BglA9 from Anoxybacillus ayderensis A9 and its application in de-glycosylation of Polydatin.

This study reports a novel BglA9 gene of 1345 bp encoding ß-glucosidase from Anoxybacillus ayderensis A9, which was amplified and expressed in E. coli BL21 (DE3): pLysS cells, purified with Ni-NTA column having molecular weight of 52.6 kDa and was used in the bioconversion of polydatin to resveratrol. The kinetic parameters values using pNPG as substrate were Km (0.28 mM), Vmax (43.8 µmol/min/mg), kcat (38.43 s-1) and kcat/Km (135.5 s-1 mM-1). The BglA9 was active in a broad pH range and had an activity half-life around 24 h at 50 °C. The de-glycosylation efficiency of BglA9 for polydatin was determined by estimating the amount of glucose released after enzymatic reaction by a dinitrosalicylic acid (DNS) assay. The kinetic parameters of BglA9 for polydatin were 5.5 mM, 20.84 µmol/min/mg, 18.28 s-1and 3.27 s-1 mM-1 for Km, Vmax, kcat, and kcat/Km values, respectively. The Ki value for glucose was determined to be 1.7 M. The residues Gln19, His120, Glu355, Glu409, Glu178, Asn222 may play a crucial role in the deglycosylation as revealed by the 3D structure of enzyme docked with polydatin.

Nonomuraea insulae sp. nov., isolated from forest soil.

Strain H2R21T, a novel actinobacterium, isolated from a forest soil sample collected from Heybeliada, Istanbul, Turkey, and a polyphasic approach was used for characterisation of the strain. Chemotaxonomic and morphological characterisation of strain H2R21T indicated that it belongs to the genus Nonomuraea. 16S rRNA gene sequence similarity showed that the strain is closely related to Nonomuraea purpurea 1SM4-01T (99.1%) and Nonomuraea solani CGMCC 4.7037T (98.4%). DNA-DNA relatedness values were found to be lower than 70% between the isolate and its phylogenetic neighbours N. purpurea 1SM4-01T, N. solani CGMCC 4.7037T and Nonomuraea rhizophila YIM 67092T. The whole cell hydrolysates of strain H2R21T were found to contain meso-diaminopimelic acid as the diagnostic diamino acid and glucose, madurose, mannose and ribose as the cell sugars. The polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, dihydroxy-phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, two glycophospholipids and two unidentified lipids. The predominant menaquinones were identified as MK-9(H4) and MK-9(H6). The major fatty acids were found to be iso-C16:0, iso-C16:0 2OH and C17:0 10-methyl. On the basis of DNA-DNA relatedness data and some phenotypic characteristics, it is evident that strain H2R21T can be distinguished from the closely related species in the genus Nonomuraea. Thus, it is concluded that strain H2R21T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea insulae sp. nov. is proposed. The type strain is H2R21T (= DSM 102915T = CGMCC 4.7338T = KCTC 39769T).

Saccharopolyspora hattusasensis sp. nov., isolated from soil.

A Saccharopolyspora strain, designated CR3506T, isolated from a soil sample collected from Sungurlu, Corum, Turkey, was examinated using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence analysis showed that the strain is closely related to the type strains of Saccharopolyspora spinosa NRRL 18395T (99.1%), Saccharopolyspora phatthalungensis NRRL B-24798T (98.4%) and Saccharopolyspora shandongensis 88T (98.1%); low levels of DNA-DNA relatedness were found between the isolate and S. spinosa and S. phatthalungensis (<50%). Strain CR3506T was found to have chemotaxonomic and phylogenetic properties consistent with its classification in the genus Saccharopolyspora. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The polar lipids were identified as phosphatidylmethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones (>10%) were MK-9(H4) and MK-8(H4). Major fatty acids were (>10%) iso-C16:0, C15:03OH, C18:0 and iso-C15:0. Further, the morphological, physiological and biochemical characteristics of strain CR3506T are distinct from S. spinosa and other species of the genus Saccharopolyspora with which this strain has high 16S rRNA gene sequence similarity (98.0-98.5%). Strain CR3506T has antimicrobial activity against Bacillus subtilis NRRL B-209, Citrobacter freundi NRRL B-2643 and Staphylococcus aureus ATCC 29213. Consequently, it is proposed that strain CR3506T represents a novel Saccharopolyspora species for which the name Saccharopolyspora hattusasensis sp. nov. is proposed. The type strain is CR3506T (=KCTC 29104T = DSM 45715T).

Redesigning pH optimum of Geobacillus sp. TF16 endoxylanase through in silico designed DNA swapping strategy.

Thermoalkaliphilic xylanases are highly desired and of great importance due to their vast potential in paper pulp and bleaching processes. Here, we report rapid, cost-effective, and result-oriented combinatorial potential of in silico DNA swapping strategy to engineer the pH optimum of industrially crucial enzymes, particularly engineering of Geobacillus sp. TF16 endoxylanase for alkaline environments. The 3D structures of Geobacillus sp. TF16 and donor Bacillus halodurans C-125 endoxylanases were firstly predicted, analyzed, and compared for their similarities before any in silico design of mutants. Reasonably, to improve its alkaline pH tolerance, the corresponding regions in Geobacillus sp.TF16 endoxylanase were further engineered by swapping with negatively-charged amino acid-rich regions from B. halodurans C-125 endoxylanase. Through only two of four in silico-designed mutants, the optimum pH of GeoTF16 endoxylanase was improved from 8.5 to 10.0. Moreover, as compared to GeoTF16 parental enzyme, both GeoInt3 and GeoInt4 mutants revealed (i) enhanced biobleaching performance, (ii) improved adaptability to alkaline conditions, and (iii) better activity for broader pH range. Unlike GeoTF16 losing activity at pH 11.0 completely, GeoInt4 retained 60% and 40% of its activity at pH 11.0 and 12.0, respectively. Thus, GeoInt4 stands out as a more competent biocatalyst that is suitable for alkaline environments of diverse industrial applications. The current study represents an efficient protein engineering strategy to adapt industrial catalysts to diverse processing conditions. Further comprehensive and fine-tuned research efforts may result in biotechnologically more promising outcomes.

Fontibacillus pullulanilyticus sp.nov. isolated from soil.

Gram stain-negative, motile, catalase-, and oxidase- positive strain, designated DSHK107(T) was isolated from soil of Cukurova University campus in Adana, Turkey. Its taxonomy was investigated using a polyphasic approach. The strain grew at 20-42 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in 0-2.0% NaCl (w/v). 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Fontibacillus; strain DSHK107(T) showed highest sequence similarity to type strains Fontibacillus aquaticus GPTSA 19(T) (97.8%) and Fontibacillus panacisegetis P11-6(T) (97.0%). The major fatty acid of strain DSHK107(T) was anteiso-C15:0 (46.7). The polar lipids of strain DSHK107(T) consisted of dihosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids, four unknown lipids, three unknown glycolipids, two unknown aminophospholipids, an unknown aminolipid, and an unknown aminophosphoglycolipid. The major isoprenoid quinone was MK-7. The DNA G+C content of DSHK107(T) was 42.1 mol%. DNA-DNA hybridization showed that the strain DSHK107(T) shared low DNA-DNA relatedness with F. aquaticus DSM 17643(T) , Fontibacillus solani A4STRO4(T) , and F. panacisegetis DSM 28129(T) (47, 58, and 59.3%, respectively). Thus, our results support the placement of strain DSHK107(T) within a separate and previously unrecognized species. On the basis of a taxonomic study using a polyphasic approach, strain DSHK107(T) is considered to represent a novel species of the genus Fontibacillus, for which the name Fontibacillus pullulanilyticus sp. nov. is proposed. The type strain is DSHK107(T) (=NCCB 100560(T) = DSM 100116(T) ).