Laboratoire de Valorisation et Conservation des Ecosystèmes Arides (LVCEA), Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaia, B.P. 455, Ghardaïa 47000, Algeria.
Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers 16308, Algeria.
Genes (Basel). 2024 Sep 12;15(9):1202. doi: 10.3390/genes15091202.
This study aims to evaluate the in silico genomic characteristics of five species of the genus : , , , , and , with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.5%, while OrthoANI values were lower than 95.3%, suggesting that the five species represent distinct genomospecies. These results were consistent with the phylogenomic study based on core genes and the pangenome analysis of these five species within the genus . However, the genome annotation showed some differences between these species, such as variations in the number of subsystem category distributions across whole genomes (ranging between 1979 and 2024). Additionally, the number of CAZYme (Carbohydrate-Active enZYme) genes ranged between 298 and 325, highlighting the potential of these bacteria for therapeutic research applications. The in silico physico-chemical characteristics of cellulases from species were analyzed. Their 3D structure was modeled, refined, and validated. A molecular docking analysis of this cellulase protein structural model was conducted with cellobiose, cellotetraose, laminaribiose, carboxymethyl cellulose, glucose, and xylose ligand. Our study revealed significant interaction between the cellulase and cellotetraose substrate, evidenced by stable binding energies. This suggests that this bacterial enzyme holds great potential for utilizing cellotetraose as a substrate in various applications. This study enriches our understanding of the potential applications of species in therapeutic research.
、、、、和，以期将其应用于治疗研究。16S rRNA 比较表明这些物种在系统发育上是不同的。这些研究的模式菌株之间的数字 DNA-DNA 杂交（dDDH）和 OrthoANI 值的成对比较表明 dDDH 值低于 62.5%，而 OrthoANI 值低于 95.3%，表明这五个物种代表不同的基因组种。这些结果与基于核心基因的系统基因组研究和属内这五个物种的泛基因组分析一致。然而，基因组注释显示这些物种之间存在一些差异，例如整个基因组中亚系类别分布数量的变化（范围在 1979 到 2024 之间）。此外，CAZYme（碳水化合物活性酶）基因的数量在 298 到 325 之间，这突出了这些细菌在治疗研究应用中的潜力。分析了 物种纤维素酶的计算物理化学特性。对其 3D 结构进行建模、细化和验证。对该纤维素酶蛋白结构模型与纤维二糖、纤维四糖、纤维三糖、羧甲基纤维素、葡萄糖和木糖配体进行了分子对接分析。我们的研究揭示了 纤维素酶与纤维四糖底物之间存在显著的相互作用，这表现为稳定的结合能。这表明这种细菌酶在各种应用中利用纤维四糖作为底物具有巨大的潜力。本研究丰富了我们对 物种在治疗研究中潜在应用的理解。
