Characterization of urease active calcite-producing strain YX-3 combined with the whole genome.

Autor: Zhang S; College of Life Science, Northwest University, 229 Tai bai North Rd, Xi'an, Shaanxi, 710069, China; Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China., Liu S; College of Life Science, Northwest University, 229 Tai bai North Rd, Xi'an, Shaanxi, 710069, China., Chen M; College of Life Science, Northwest University, 229 Tai bai North Rd, Xi'an, Shaanxi, 710069, China., Lu J; College of Life Science, Northwest University, 229 Tai bai North Rd, Xi'an, Shaanxi, 710069, China., Ma Y; College of Life Science, Northwest University, 229 Tai bai North Rd, Xi'an, Shaanxi, 710069, China; Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China. Electronic address: mayanling@nwu.edu.cn.
Jazyk: angličtina
Zdroj: Environmental research [Environ Res] 2024 Dec 01; Vol. 262 (Pt 1), pp. 119855. Date of Electronic Publication: 2024 Aug 27.
DOI: 10.1016/j.envres.2024.119855
Abstrakt: Urease found in a wide range of microorganisms plays a vital role in ureolytic induced calcite precipitation (UICP). However, the genomic information on urease-producing strains is limited, and there is a need for further in-depth studies on aspects such as the regulation of urease activity by nickel ligand residues. The present study delved into the elucidation of urease activity in a newly isolated strain YX-3 coupled with nickel-ligand residues by employing the genetic architecture of biomineralization-controlled growth, molecular docking, molecular dynamics simulation (MDS), and site-directed mutagenesis. Genome-wide sequencing showed the presence of urease gene clusters, comprising structural genes ureA, ureB, and ureC, alongside auxiliary genes ureD, ureE, ureF, and ureG. RT-qPCR analysis showed that the addition of NiCl 2 resulted in a significant up-regulation of ureC expression. His267, His294, and Gly325 in the domain of UreC were further proved to coordinate with nickel ions and urea simultaneously through homology modeling and molecular docking, and molecular dynamics simulations (MDS) showed the urease-urea docking complexes exhibited degressive binding stability by four metrics including root mean square deviations (RMSD) when those residues were mutated into alanine respectively. Western blotting exhibited that mutations of H267A, H294A, and G325A led to a reduction in the relative expression of urease, wherein urease activity was about 62%, 45%, and 20% times that of the wild type (WT), respectively. The overexpression results further confirmed the importance of these residues for urease activity and CaCO 3 precipitation. These results would help to deepen the understanding of urease-producing strains at a molecular level and expand the theoretical basis for modulating urease activity.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2024 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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