Characterization of a Bacillus megaterium strain with metal bioremediation potential and in silico discovery of novel cadmium binding motifs in the regulator, CadC

• Published in: Applied microbiology and biotechnology 2021-03, Vol.105 (6), p.2573-2586
• Main Authors: Kumari, Weerasingha Mudiyanselage Nilmini Hasintha, Thiruchittampalam, Shalini, Weerasinghe, Mahinagoda Siril Samantha, Chandrasekharan, Naduviladath Vishvanath, Wijayarathna, Champika Dilrukshi
• Format: Article
• Language: English
• Subjects: Aspartic acid; Bacillus (Bacteria); Bacillus megaterium; Bacillus megaterium - genetics; Bacteria; Bacterial Proteins - genetics; Binding sites; Binding sites (Biochemistry); Biodegradation, Environmental; Biomedical and Life Sciences; Bioremediation; Biotechnology; Cadmium; Chemical properties; Computer Simulation; Control; Copper; Crystal structure; Detoxification; Efflux; Environmental Biotechnology; Genetic aspects; Heavy metals; Homology; Identification and classification; Industrial effluents; Industrial wastewater; Innovations; Lead; Life Sciences; Metal ions; Methods; Microbial Genetics and Genomics; Microbiology; Microorganisms; Molecular dynamics; Open reading frames; Proteins; Repressor Proteins; RNA, Ribosomal, 16S; rRNA 16S; Staphylococcus aureus - genetics; Zinc
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-021-11193-2

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 Cd 2+ and Zn 2+ 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 (Cd 2+ ).