Abstract
The deluge of sequence information in the recent times provide us with an excellent opportunity to compare organisms on a large genomic scale. In this study we have tried to decipher the variation in the gene organization and structuring of a vital bacterial gene called ftsZ which codes for an integral component of the bacterial cell division, the FtsZ protein. FtsZ is homologous to tubulin protein and has been found to be ubiquitous in eubacteria. FtsZ is showing increasing promise as a target for antibacterial drug discovery. Our study of ftsZ protein from 143 different bacterial species spanning a wider range of morphological and physiological type demonstrates that the ftsZ gene of about ninety three percent of the organisms show relatively biased codon usage profile and significant GC deviation from their genomic GC content. Comparative codon usage analysis of ftsZ and a core housekeeping gene rpoB demonstrated that codon usage pattern of ftsZ CDS is shaped by natural selection to a large extent and mimics that of a housekeeping gene. We have also detected a tendency among the different organisms to utilize a core set of codons in structuring the ftsZ coding sequence. We observed that the compositional frequency of the amino acid serine in the FtsZ protein appears to be a indicator of the bacterial lifestyle. Our meticulous analysis of the ftsZ gene linked with the corresponding FtsZ protein show that there is a bias towards the use of specific synonymous codons particularly in the helix and strand regions of the multi-domain FtsZ protein. Overall our findings suggest that in an indispensable and vital protein such as FtsZ, there is an inherent tendency to maintain form for optimized performance in spite of the extrinsic variability in coding features.
Highlights
Codon usage bias (CUB) or the preference of an organism for a certain subset of codons coding for the different amino acids of polypeptides is an important evolutionary feature that has intrigued molecular biologists and evolutionists for decades [1,2]
After analysing the codon usage data of ftsZ given in S2 Table from the 142 species we found that Kocuria kristinae, which is a pathogenic, Gram-positive bacteria exhibits the lowest number of codons (Nc) value (24.56) among all the organisms
Our study of the gene sequences coding for ftsZ gene and its corresponding protein (FtsZ) from 142 bacterial species demonstrated that about one third of the selected organisms depicted more than ten percent GC variation in their ftsZ coding sequences (CDS) compared to their genomic GC content
Summary
Codon usage bias (CUB) or the preference of an organism for a certain subset of codons coding for the different amino acids of polypeptides is an important evolutionary feature that has intrigued molecular biologists and evolutionists for decades [1,2]. It is a universal phenomenon observed in prokaryotes, eukaryotes [3] as well as viruses [4], and is predominantly dependent on selection, mutation, and genetic drift [5]. The higher-order structure of FtsZ protein in vitro includes ribbons, sheets and bundles [46,47,48]
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