In this study, 16S rRNA of diarrhoea microbial cluster was investigated computationally. The phylogeny, two- and three-dimensional structures, molecular docking and dynamics simulations were carried out. The result showed that Escherichia coli, Campylobacter jejuni, Campylobacter upsaliensis, Streptococcus lutetiensis 033, Streptococcus infantarius, Enterococcus ratti, Helicobacter sp. 'feline isolate, Helicobacter canadensis, Anaerobiospirillum sp. B0101, Anaerobiospirillum sp. 3J102 as well as uncultured bacterium (Prevotella) and unidentified bacterium (Lactobacillus) were involved in diarrhoea infection. Optimal secondary structure alignment from ClustalO has a minimum free energy (MFE) of -764.31 kcal/mol while that Aligner has MFE of -592.43 kcal/mol. The free energies from molecular docking reveal possible efficacy in the order of doxycycline > metacycline > streptomycin > rolitetracycline > tetracycline > tigecycline. Out of 17 antibiotics used in this study, chlortetracycline and minocycline have high affinity for methyltransferase KsgA (PDB ID: 3TPZ), kanamycin has almost equal affinity for both enzymes, while the remaining 14 antibiotic compounds have high affinity for pseudouridine synthase RsuA (PDB ID: 1KSV). The modelled three-dimensional structure of 16S rRNA bind to 1KSV and 3TPZ with free energy of -367.52 kcal/mol and-371.55 kcal/mol respectively. Moreover, the active site nucleotide residues were found to have direct interaction with amino acid residues in the active site of the enzymes. This study provides insight on the mechanism of action of antibiotics that targeted 16S rRNA by inhibition of key enzymes that involve in protein synthesis.
Thermostable enzymes have found applications in the improvement of products quality in various industries. Despite the discovery of several microorganisms as potential source of thermostable enzymes, more biodiversity explorations are currently been carried out for high activity enzymes producing isolates. The discovery of new isolates having these characters will allow to efficiently carry out reactions in various industrial processes that involve extreme conditions. This study was aimed to screen and isolate thermophilic fungi from three selected compost wastes sites (Palm oil mill, Wood chip piles and Abattoir dump), and identify potential producers of lipases, cellulases and proteases respectively. The thermophilic fungi were obtained from an equal depth of one meter in all the three collection sites with a temperature range of 40 to 45OC and later cultured at 70 OC. Further experimental screening analysis showed the presences of lipase, cellulase and protease producing fungi present in samples collected from palm oil mill, wood chips pills and abattoir dump site respectively. The isolated fungi were used for enzyme production in submerged fermentation for 10 days at 50OC. Culture filtrate obtained from the medium of production were used for the assessment of enzymatic activity. The highest lipase, cellulase and protease activities were obtained from isolates 3 A (56.56 U/mL), 3A (38.35 U/mL) and 2B (3.0 U/mL) respectively. These isolates with high enzymes activities were identified microscopically as Rhizopus sp., Aspergillus flavus and Neurospora sp. accordingly. We believed that these strains could be further exploited for numerous industrial applications that require thermophilic enzymes.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a microorganism that causes coronavirus disease 2019 (COVID-19). Mutations affect evolutionary conservation of microorganisms. The fast pace evolutionary changes are currently affecting pathogenicity of SARS-CoV-2. In this study, the structural fluctuations of the amino acid residues in the spike glycoprotein and RNA-dependent RNA polymerase (nsp12) of SARS-CoV-2 were investigated by in silico approach using structural flexibility dynamics to decipher susceptibility to mutation. The result of this study implicated key amino acid residues (with rmsf) which could be very susceptible to mutation, which include residues 50 (3.79 Å), 119 (4.56 Å), 120 (3.53 Å), 220 (3.84 Å), 265 (4.31 Å) of RNA-dependent RNA polymerase (nsp12), as well as residues 477 (4.21 Å), 478 (4.82 Å), 479 (5.40 Å), 481 (5.94 Å), 560 (4.63 Å), 704 (4.02 Å), 848 (4.58 Å), 1144 (4.56 Å) and 1147 (4.61 Å) of spike glycoprotein. The SARS-CoV-2 mutations destabilized the overall protein structure in multiples of amino acid residues which could interfere with active site leading to insensitivity or resistance to the inhibitors. Mutation T478K of Spike glycoprotein showed the highest deviation in the structure. Overall, spike glycoprotein has the highest number of mutations, and these variants could increase the risk to human health if not mitigated in the population.
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