title: Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes.
abstract: Our environment is stressed with a load of heavy and toxic metals. Microbes, abundant in our environment, are found to adapt well to this metal-stressed condition. A comparative study among five Cupriavidus/Ralstonia genomes can offer a better perception of their evolutionary mechanisms to adapt to these conditions. We have studied codon usage among 1051 genes common to all these organisms and identified 15 optimal codons frequently used in highly expressed genes present within 1051 genes. We found the core genes of Cupriavidus metallidurans CH34 have a different optimal codon choice for arginine, glycine and alanine in comparison with the other four bacteria. We also found that the synonymous codon usage bias within these 1051 core genes is highly correlated with their gene expression. This supports that translational selection drives synonymous codon usage in the core genes of these genomes. Synonymous codon usage is highly conserved in the core genes of these five genomes. The only exception among them is C. metallidurans CH34. This genomewide shift in synonymous codon choice in C. metallidurans CH34 may have taken place due to the insertion of new genes in its genomes facilitating them to survive in heavy metal containing environment and the co-evolution of the other genes in its genome to achieve a balance in gene expression. Structural studies indicated the presence of a longer N-terminal region containing a copper-binding domain in the cupC proteins of C. metallidurans CH3 that helps it to attain higher binding efficacy with copper in comparison with its orthologs.
authors.affiliation: a Apt Software Avenues Pvt. Ltd, Unit G 301, Block DC , City Centre , Sector I, Salt Lake, Kolkata 700064 , India.
authors.forename: Pratim
authors.initials: P
authors.lastname: Chakraborti
authors.affiliation: b Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India.
authors.forename: Rachana
authors.initials: R
authors.lastname: Banerjee
authors.affiliation: c NBU Bioinformatics Facility, Department of Botany , University of North Bengal , Raja Rammohanpur, Siliguri 734013 , India.
authors.forename: Ayan
authors.initials: A
authors.lastname: Roy
authors.affiliation: b Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India.
authors.forename: Sunanda
authors.initials: S
authors.lastname: Mandal
authors.affiliation: b Department of Biophysics, Molecular Biology and Bioinformatics , University of Calcutta , 92, A.P.C. Road, Kolkata 700009 , India.
authors.forename: Subhasish
authors.initials: S
authors.lastname: Mukhopadhyay
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D003062:Codon; D019295:Computational Biology; D049921:Cupriavidus / Q000235:genetics* / Q000378:metabolism; D024881:Drug Resistance, Bacterial; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D000075322:Heavy Metal Poisoning; D008670:Metals / Q000737:chemistry* / Q000378:metabolism / Q000633:toxicity; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011041:Poisoning; D011485:Protein Binding; D021281:Quantitative Structure-Activity Relationship; D043367:Ralstonia / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D008670:Metals
keywords: core genes; gene expression; heavy metal resistance; optimal codons; potential energy; structural stability; synonymous codon usage bias; tertiary structure