Nickel-Driven Dynamics of Urease in Sporosarcina pasteurii: Integrated Computational and Experimental Insights

Abstract

Urease is a nickel-dependent enzyme that plays an important role in urea hydrolysis and in a process named as microbial-induced calcium carbonate precipitation (MICP), which is widely used in sustainable environmental biotechnology. Despite its ecological importance, urease powers Biogrout (biocementation), a promising green technology for soil stabilization and infrastructure repair. Yet, the relationship between nickel availability, enzyme activation, and bacterial fitness remains poorly understood. In this study, we reveal a striking dual effect of nickel on Sporosarcina pasteurii: while high Ni{superscript 2} concentrations strongly inhibit growth (IC {approx} 637.7 {micro}M), they simultaneously boost specific urease activity up to six-fold. This uncoupling between biomass and enzymatic efficiency highlights a previously overlooked adaptive strategy under metal stress. Using structural bioinformatics and molecular docking, we show that Ure1--the catalytic subunit--exhibits the strongest nickel affinity (-4.3 kcal{middle dot}mol-{superscript 1}), supported by highly conserved active-site residues, whereas accessory proteins UreE and UreG display moderate and weak binding, consistent with their roles in metal delivery and GTP-dependent maturation. In addition, microscopic observations confirmed that calcium carbonate precipitation was most pronounced at intermediate nickel concentrations (approximately 400-1000 {micro}M), whereas higher concentrations ([≥]1000-1300 {micro}M) led to reduced mineral formation due to loss viable cells. Taken together, these results indicates that nickel availability controls both urease activation and bacterial fitness, and that an optimal balance is required to maximize biomenerilization efficiency in environmental applications, particularly in biocementation technology. ImportanceUrease-driven biomineralization is widely used in sustainable technologies such as soil stabilization and self-healing concrete. However, optimizing these systems requires a clear understanding of how environmental factors influence enzyme performance. This study shows that nickel, an essential cofactor for urease, plays a dual role by enhancing enzymatic activity while inhibiting bacterial growth at high concentrations. By integrating experimental data with computational analysis, we demonstrate that efficient biomineralization depends on maintaining nickel within an optimal range that balances enzyme activation and microbial viability. These findings provide practical guidance for improving biocementation processes and highlight nickel as a key regulator of urease-based environmental biotechnology applications.