Abstract
Bioremediation of toxic metal ions using bacterial strains is a promising tool. Metal binding motifs in microbial proteins are involved in the regulation and transport of such toxic metals for metal detoxification. A bacterial strain designated TWSL_4 with metal (Cu, Cd, and Pb) resistance and removal ability was isolated and identified as a Bacillus megaterium strain using 16S rRNA gene analysis. An operon with 2 open reading frames (ORFs) was identified, cloned, and sequenced. ORF1 and ORF2 were identical to the cadmium efflux system accessory protein (CadC) and cadmium-translocating P-type ATPases (CadA) of B. megaterium strain YC4-R4 respectively. A protein homology search using Swiss model retrieved no crystal structures for CadC and CadA of Bacillus sp.. CadC of TWSL_4 had a sequence identity of 53% to the CadC (121aa) protein and 51.69% to the CadC crystal structure (1U2W.1.B; GMQE=0.75) of Staphylococcus sp. pI258. Molecular dynamic simulation studies revealed the presence of three metal binding regions in CadC of TWSL_4, [ASP7-TYR9], [ASP100-HIS102], and [LYS113-ASP116]. This is the first report showing evidence for the presence of Cd2+ and Zn2+ metal binding motifs in the CadC regulator of the Bacillus megaterium cad operon. The bacterial strain TWSL_4 was also found to contain two different P type ATPases encoding genes, cadA and zosA involved in metal resistance. Furthermore, the metal bioremediation potential of strain TWSL_4 was confirmed using an industrial effluent.
Key points
• Isolation of a metal-resistant bacterial strain with potential for industrial bioremediation.
• Discovery of novel Cd binding sites in CadC of the cad operon from B. megaterium.
• Involvement of aspartic acid in the coordination of metal ions (Cd2+).
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Data availability
The nucleotide sequence data used to support the findings of this study are deposited in the NCBI repository. (GenBank accession no: KR027922.1 [16S rRNA gene]; KY366323.1 [cadA partial gene]; KY366324.1 [zosA partial gene]; MK327282.1 [Cadmium resistant system/ ORFs of cadCA operon]). Bacterial (wild type) strain used in this study (Bacillus megaterium TWSL_4) is deposited in the NBRC culture collection repository with the culture collection number NBRC 114811.
Code availability
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Acknowledgements
We gratefully acknowledge Mr. P. G. W. Ariyasena (Department of Chemistry, University of Colombo, Sri Lanka) for his assistance in operating the AAS.
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This work was funded by the research grant RG/2012/BT/08, National Science Foundation of Sri Lanka.
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CDW and NVC conceptualized, designed, and supervised the research. NHK conducted experiments. NHK analyzed data and wrote the manuscript. ST and MSSW contributed to computational analysis. All authors read and approved the manuscript.
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Kumari, W.M.N.H., Thiruchittampalam, S., Weerasinghe, M.S.S. et al. Characterization of a Bacillus megaterium strain with metal bioremediation potential and in silico discovery of novel cadmium binding motifs in the regulator, CadC. Appl Microbiol Biotechnol 105, 2573–2586 (2021). https://doi.org/10.1007/s00253-021-11193-2
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DOI: https://doi.org/10.1007/s00253-021-11193-2