Revision as of 18:07, 1 October 2024

UreA-UreB-UreC

Usage

UreABC is the primary functional subunit of bacterial Urease protein,they combine to form a hetero-trimer, which binds together to create an active enzyme.When co-expressed with UreEFGD (the accessory subunit,BBa K5166065) from another part, it can produce bacterial Urease. In this project, we utilize E.coli to express this urease, enabling metal ions present in solution after sorting to precipitate in the form of carbonate, thus achieving the purpose of mineralization.

Biology

UreA, UreB, and UreC are all derived from S. pasteurii, and their sequences can be found in the following parts: UreA:BBa_K5166015;UreB:BBa_K5166016;UreB:BBa_K5166017.Microorganisms that produce urease can utilize the enzymatic activity of urease to catalyze the decomposition of urea into ammonia and carbonate, causing metal ions to precipitate into stable carbonates, effectively immobilizing these metals[1].It has been reported that the high-urease-activity strain S. pasteurii can utilize this hydrolytic capability to bind heavy metal ions in water and generate carbonate precipitates to remove heavy metals [2]. Our project precisely leverages the same principle.

Experiments

Stage 1:
Due to the excessive length of the highly efficient urease gene in S. pasteurii, we have divided it into two segments and cloned them onto corresponding plasmids separately. Specifically, UreA, UreB, and UreC are cloned onto the pET28a plasmid (with a T7 promoter), while UreE, UreF, UreG, and UreD are cloned onto the pET21b plasmid (with a proD promoter).(This page shows only the UreABC part)

Fig. 1 UreA, UreB, and UreC cloned onto the pET28a plasmid (with a T7 promoter).

However, during the preparation of the urease activity detection medium and quantitative detection, the expression of urease was not apparent. Additionally, in subsequent SDS-PAGE analysis, the protein bands were also not distinct. Therefore, we further optimized our dual-plasmid system.

Fig. 2 SDS-PAGE result of stage 1.

Stage 2:
Based on the issues encountered during Stage 1 of urease expression, we plan to make the following improvements:
Change the promoter: Replace the proD promoter preceding UreE, UreF, UreG, and UreD with the strong T7 promoter to enhance the expression of downstream genes. Concurrently, we need to optimize the induction conditions, which primarily include the concentrations of IPTG and Ni2+, as well as the induction temperature and time, to improve the activity of expressed urease. For detailed improvements regarding UreEFGD, please refer to Part：BBa K5166065
Similarly, this time we also examined the effect of urease expression through quantitative urease detection and SDS-PAGE analysis. The SDS-PAGE result is shown in Fig.3, while the principle and results of the quantitative urease detection are presented in Fig.4.The urease activity is 0.153U/g DCW（U：the amount of enzyme that catalyzes the formation of 1.0 µmole of ammonia per minute at pH 7.0.）

Fig. 3 SDS-PAGE result of stage 2.

Fig. 4 The principle and results of the quantitative urease detection.

Through the above experimental investigations, we have improved the recombinant expression of urease, and measurements have confirmed that the recombinant urease is active. Stage 3:Mineralization Validation Experiment
We conducted a series of validation experiments, and some of the more representative results are as follows:
1.Optical Microscope Observation
As can be seen from Fig.5, compared to the BL21(DE3) control group, the dual-plasmid experimental group with recombinant urease exhibits significant differences in the mineralization of four metal ions: Li, Mn, Co, and Ni, under optical microscopy. Specifically, the bacteria in the experimental group show noticeable agglomeration and clustering, and a layer of material is clearly attached around the bacteria.

Fig. 5 Optical Microscope Observation of Biomineralization Results.

2.SEM/EDS analysis
Since the biomineralization of calcium carbonate is the most prevalent, we first used the biomineralization of Ca2+ as an example to verify the mineralization level of the recombinant urease. For the SEM and EDS analysis of Mn, Co, and Ni, please refer to our wiki result interface (due to the limitations of scanning electron microscopy, EDS cannot analyze elements lighter than carbon, so Li cannot be analyzed by EDS).

Fig. 6 SEM Image of Ca2+ Biomineralization Results.

Fig. 7 SEM images of Ca2+ biomineralization results (Note: Negative control is biomineralization by co-incubation with metal ions using wild-type BL21 bacteria without urease double plasmid; Positive control is simulated in vitro biomineralization by adding urease in addition to wild-type BL21 bacteria; Experimental group is the biomineralization of BL21 bacteria with recombinantly expressed double plasmid containing urease in the present project) a) Electromicrograph of Ca negative control；b) Electromicrograph of Ca Electron micrograph of experimental group；c) Electron micrograph of Ca positive control.

Reference

[1]Fang L, Niu Q, Cheng L, et al. Ca-mediated alleviation of Cd2+ induced toxicity and improved Cd2+ biomineralization by Sporosarcina pasteurii[J]. Science of The Total Environment, 2021, 787: 147627.（https://www.sciencedirect.com/science/article/pii/S004896972102698X）
[2] Li M, Cheng X, Guo H. Heavy metal removal by biomineralization of urease producing bacteria isolated from soil[J]. International Biodeterioration & Biodegradation, 2013, 76: 81-85.（https://www.sciencedirect.com/science/article/pii/S0964830512001497）

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal XbaI site found at 47
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 129
21
COMPATIBLE WITH RFC[21]
23
INCOMPATIBLE WITH RFC[23]
Illegal XbaI site found at 47
25
INCOMPATIBLE WITH RFC[25]
Illegal XbaI site found at 47
Illegal AgeI site found at 514
Illegal AgeI site found at 1055
Illegal AgeI site found at 2485
1000
COMPATIBLE WITH RFC[1000]