Cloning, sequence analysis, and molecular docking of nuclease B from Bacillus paralicheniformis str. PMp/10

IF 1 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2024-06-04 DOI:10.1016/j.genrep.2024.101944

Maha T.H. Emam , Ahmad A. Radwan , Osama M. Darwesh , Hala M. Abu Shady , Karima A. Mohamed

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引用次数: 0

Abstract

Bacterial biofilms cause serious problems in the industrial sector and human healthcare. Nucleases are characterized as biofilm-degrading enzymes. In this work, the extracellular nuclease nucB gene from a new isolate Bacillus paralicheniformis str. PMp/10 was isolated and cloned successfully into the cloning vector pET 29a⁺, then transformed into E. coli DH5α. The nucB gene has a molecular weight of 429 bp, its sequence was uploaded to the NCBI GenBank database under the accession number OP712506 which is the first report for B. paralicheniformis. The gene encoded a nuclease B enzyme consisting of 142 amino acids with an estimated molecular weight of 13 kDa. The 3D and 2D structure of nuclease B was predicted and the NucB enzyme's secondary structure prediction showed that it has five β-strands and three α-helices. Finally, the Molecular docking interaction between NucB and deoxyribonucleic acid was performed successfully with a high binding affinity (−7.1 kcal/mol).

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副嗜血杆菌核酸酶 B 的克隆、序列分析和分子对接PMp/10

细菌生物膜给工业领域和人类医疗保健带来了严重问题。核酸酶是生物膜降解酶的一种。在这项工作中，我们从一种新分离的副溶血性芽孢杆菌（Bacillus paralicheniformis str.PMp/10 中分离出来，并成功克隆到克隆载体 pET 29a+ 中，然后转化到大肠杆菌 DH5α 中。nucB 基因的分子量为 429 bp，其序列已被上传到 NCBI GenBank 数据库，登录号为 OP712506，这是首次报告副银环蛇菌的 nucB 基因。该基因编码的核酸酶 B 由 142 个氨基酸组成，分子量约为 13 kDa。对核酸酶 B 的三维和二维结构进行了预测，NucB 酶的二级结构预测表明它有 5 个 β 链和 3 个 α 螺旋。最后，成功地进行了 NucB 与脱氧核糖核酸之间的分子对接相互作用，其结合亲和力很高（-7.1 kcal/mol）。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.