Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
Department of Sciences, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, 10300, Thailand.
World J Microbiol Biotechnol. 2023 Oct 19;39(12):348. doi: 10.1007/s11274-023-03805-y.
Over recent years, Alicyclobacillus acidocaldarius, a Gram-positive nonpathogenic rod-shaped thermo-acid-tolerant bacterium, has posed numerous challenges for the fruit juice industry. However, the bacterium's unique characteristics, particularly its nonpathogenic and thermophilic capabilities, offer significant opportunities for genetic exploration by biotechnologists. This study presents the computational proteogenomics report on the carboxylesterase (CE) enzyme in A. acidocaldarius, shedding light on structural and evolutional of CEs from this bacterium. Our analysis revealed that the average molecular weight of CEs in A. acidocaldarius was 41 kDa, with an isoelectric point around 5. The amino acid composition favored negative amino acids over positive ones. The aliphatic index and hydropathicity were approximately 88 and - 0.15, respectively. While the protein sequence showed no disulfide bonds in the CEs' structure, the presence of Cys amino acids was observed in the structure of CEs. Phylogenetic analysis presented more than 99% similarity between CEs, indicating their close evolutionary relationship. By applying homology modeling, the 3-dimensional structural models of the carboxylesterase were constructed, which with the help of structural conservation and solvent accessibility analysis highlighted key residues and regions responsible for enzyme stability and conformation. The specific patterns presented the total solvent accessibility of less than 25 (Å) was in considerable position as well as Gly residues were noticeably have high accessibility to solvent in all structures. Ala was the more frequent amino acids in the conserved-SASA of carboxylesterases. Furthermore, unsupervised agglomerative hierarchical clustering based on solvent accessibility feature successfully clustered and even distinguished this enzyme from proteases from the same genome. These findings contribute to a deeper understanding of the nonpathogenic A. acidocaldarius carboxylesterase and its potential applications in biotechnology. Additionally, structural analysis of CEs would help to address potential solutions in fruit juice industry with utilization of computational structural biology.
近年来，具有革兰氏阳性、非致病性、杆状、耐热耐酸特性的嗜酸热脂环酸芽孢杆菌给果汁行业带来了诸多挑战。然而，该细菌的独特特性，特别是其非致病性和耐热性，为生物技术人员进行遗传探索提供了重要机会。本研究介绍了嗜酸热脂环酸芽孢杆菌中羧酸酯酶（CE）的计算蛋白质组学报告，阐明了该细菌中 CEs 的结构和进化。我们的分析表明，嗜酸热脂环酸芽孢杆菌中 CEs 的平均分子量为 41 kDa，等电点约为 5。氨基酸组成偏向于带负电荷的氨基酸而不是带正电荷的氨基酸。脂肪指数和约为 88 和-0.15。虽然蛋白质序列中 CEs 的结构没有二硫键，但在 CEs 的结构中观察到了 Cys 氨基酸的存在。系统发育分析表明，CEs 之间的相似度超过 99%，表明它们具有密切的进化关系。通过同源建模，构建了羧酸酯酶的三维结构模型，通过结构保守性和溶剂可及性分析，突出了关键残基和区域，这些残基和区域对酶的稳定性和构象起着重要作用。特定模式表明，总溶剂可及性小于 25（Å）的位置相当，并且在所有结构中 Gly 残基对溶剂具有明显的高可及性。Ala 是羧酸酯酶保守-SASA 中更常见的氨基酸。此外，基于溶剂可及性特征的无监督凝聚层次聚类成功地对该酶进行了聚类，甚至将其与来自同一基因组的蛋白酶区分开来。这些发现有助于更深入地了解非致病性嗜酸热脂环酸芽孢杆菌羧酸酯酶及其在生物技术中的潜在应用。此外，CEs 的结构分析将有助于利用计算结构生物学解决果汁行业的潜在问题。
