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. 2023 Sep 9;11(9):2262.
doi: 10.3390/microorganisms11092262.

An In Silico Bioremediation Study to Identify Essential Residues of Metallothionein Enhancing the Bioaccumulation of Heavy Metals in Pseudomonas aeruginosa

Munazzah Tasleem  1 , Wesam M Hussein  2 , Abdel-Aziz A A El-Sayed  3 , Abdulwahed Alrehaily  3
Affiliations

An In Silico Bioremediation Study to Identify Essential Residues of Metallothionein Enhancing the Bioaccumulation of Heavy Metals in Pseudomonas aeruginosa

Munazzah Tasleem et al. Microorganisms. .

Abstract

Microorganisms are ubiquitously present in the environment and exert significant influence on numerous natural phenomena. The soil and groundwater systems, precipitation, and effluent outfalls from factories, refineries, and waste treatment facilities are all sources of heavy metal contamination. For example, Madinah, Saudi Arabia, has alarmingly high levels of lead and cadmium. The non-essential minerals cadmium (Cd) and lead (Pb) have been linked to damage to vital organs. Bioremediation is an essential component in the process of cleaning up polluted soil and water where biological agents such as bacteria are used to remove the contaminants. It is demonstrated that Pseudomonas aeruginosa (P. aeruginosa) isolated from activated sludge was able to remove Cd and Pb from water. The protein sequence of metallothionein from P. aeruginosa was retrieved to explore it for physicoparameters, orthologs, domain, family, motifs, and conserved residues. The homology structure was generated, and models were validated. Docking of the best model with the heavy metals was carried out to inspect the intramolecular interactions. The target protein was found to belong to the "metallothionein_pro" family, containing six motifs, and showed a close orthologous relationship with other heavy metal-resistant bacteria. The best model was generated by Phyre2. In this study, three key residues of metallothionein were identified that participate in heavy metal (Pb and Cd) binding, viz., Ala33, Ser34, and Glu59. In addition, the study provides an essential basis to explore protein engineering for the optimum use of metallothionein protein to reduce/remove heavy metals from the environment.

Keywords: Pseudomonas aeruginosa; cadmium; in silico bioremediation; lead; molecular docking; orthologs.

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Conflict of interest statement

There are no conflict of interest to declare. We also have no financial interest to declare.

Figures

Figure 1
Figure 1
Secondary structure prediction.
Figure 2
Figure 2
Multiple sequence alignment of metallothionein from orthologous species. The highlighted columns are showing the conserved residues participating in heavy metal interaction. The horizontal green highlights are displaying the motifs. Symbols at the bottom indicate conservation and similarity levels: ‘*’ (Asterisk) for complete conservation, ‘:’ (Colon) for moderate similarity, and ‘.’ (Period) for weak similarity between aligned sequences.
Figure 3
Figure 3
(A) The UpSet table lists the number of homologous gene clusters that are both exclusive to each species and shared by all species. The figure legend explains the number of proteins in each species. (B) Venn diagram displaying the distribution of common orthologue clusters among species. The symbol “?” represents unclassified proteins not fitting in the orthologous groups. (C) Protein interaction network of the orthologous species.
Figure 3
Figure 3
(A) The UpSet table lists the number of homologous gene clusters that are both exclusive to each species and shared by all species. The figure legend explains the number of proteins in each species. (B) Venn diagram displaying the distribution of common orthologue clusters among species. The symbol “?” represents unclassified proteins not fitting in the orthologous groups. (C) Protein interaction network of the orthologous species.
Figure 4
Figure 4
Reconstructed maximum likelihood phylogeny using 37,686 all-protein samples from the seven species, with dated nodes from Time-Tree, and bootstrap index on the left side of nodes. The divergence clock is presented in million years ago at the top. The pie chart represents gene family expansion (blue) and contraction (green).
Figure 5
Figure 5
Three-dimensional modeled structures shown in cartoon presentation. (A) Model generated by GALAXY webserver, (B) model generated by LOMETS, and (C) model generated by SwissModel.
Figure 6
Figure 6
Metallothionein homology model. (A) Cartoon representation embedded on the surface view of Metallothionein (P. aeruginosa), showing two major domains. (B) Identified motifs in metallothionein represented in green color, drawn in PyMol.
Figure 7
Figure 7
(A) Interaction with Lead. (B)Interaction with Cd.
See this image and copyright information in PMC

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