Biology subjects

Deka, R. C.

Publications and source records attributed to Deka, R. C..

4 recordsLinked to original sources

bioRxiv2026

Expression-dependent but strand-independent synonymous single-nucleotide polymorphism in the Escherichia coli chromosome

AbstractMutation in genomes is mainly attributed to replication, though transcription is also known to be mutagenic and is a more frequent event than replication in an organism. Recently, there have been reports regarding genome-wide transcription-induced mutagenesis. However, a distinct demonstration of specific mutation being replication-dependent and/or transcription-dependent in genomes is yet to be established. Here, we studied synonymous single-nucleotide polymorphisms (SNPs) in 2091 individual coding sequences (CDS) in the leading strand (LeS) and the lagging strand (LaS) of the Escherichia coli chromosome by comparing across 157 strains. The frequencies of complementary transitions (ti) and complementary transversions (tv) were compared in each CDS to assess parity violation in the context of strand location and gene expression. The C[->]T and G[->]A exhibited the maximum frequency as well as the most prominent strand inequality as these tis were influenced both by the strand location as well as by the gene expression. Interestingly, inequality between T[->]C and A[->]G was expression-dependent but strand-independent. This was a direct demonstration of strand inequality due to expression but not due to replication. A[->]T and G[->]T tvs were universally more frequent than their complementary T[->]A and C[->]A, respectively. The strand-independent but expression-dependent synonymous SNP inequality in CDS, supports the role of transcription-induced mutagenesis contributing to strand inequality in the E. coli chromosome. Significance StatementMutational patterns in bacterial genomes are shaped by both replication and transcription, but their relative roles remain unclear. By analyzing synonymous SNPs across 157 strains of E. coli, we identify strong strand-specific asymmetry consistent with replication-associated biases. A strong asymmetry between the strands regarding C[->]T and G[->]A ti is observed, as it is influenced by replication asymmetry and expression. We further show that gene expression significantly influences mutation types, with T[->]C ti being enriched in the highly expressed genes and A[->]G ti being enriched in the lowly expressed genes. Notably, A[->]T ti is strand independent but exhibits mild dependency on gene expression, revealing a previously unrecognized mutational pattern. These findings highlight how some SNPs are influenced by transcription but not replication

evolutionary biology↗

bioRxiv2024

Higher frequency of transition mutation over transversion mutation in genomes: evidence from the binding energy calculation of base pairs using DFT

Base substitution mutations such as transition (ti) and transversion (tv) in organisms are major driving force in molecular evolution. In this study, different possible types of base pairing that can cause ti and tv were investigated using the density functional theory (DFT) method. The chemical structures of bases as well as base pairs were optimized using B3LYP hybrid functional along with 6-31G(d,p) basis set. We performed single point energy calculation of all optimized species using the same functional but combined with higher diffuse and polarized basis set i.e. 6-311++G(d,p) to get more refined energy of all species. The binding energy of various base pairs was calculated considering basis set superposition error (BSSE) as well as without BSSE. The binding energy of the base pairs leading to ti was found to be more stable than that of the base pairs leading to tv. This was interesting considering the observations in organisms that tis are more frequent than tvs. Among the base pairs leading to the same ti, G(keto): T (enol) base pair was found to be more stable than A(imino):C(amino) base pair. This theoretical study of binding energy of different base pairs using the DFT method has provided additional evidences in support to the biological observations of a higher transition rate than transversion in genomes.

molecular biology↗

bioRxiv2022

Modified dN/dS for accounting transition and transversion frequency difference and non-sense substitution in genomes

The dN/dS value is estimated in homologous protein coding gene sequences between two closely related organisms for studying selection on the genes. In the usual method of calculation of synonymous (S) and non-synonymous (NS) sites in codons, the transition and transversion rates are considered same as well as no difference of pretermination codons from the other codons regarding NS substitutions is considered. In this study we are proposing a modification in the method by estimating the S and the NS sites in codons by considering difference between the transition and transversion rates and the NS substitutions leading to non-sense codons in pretermination codons. So, the dN/dS value calculated by our approach was higher than that calculated by the earlier method. The modified method was applied in estimating dN/dS in 29 homologous gene sequences of Escherichia coli and Salmonella enterica. Impact of codon degeneracy and pretermination codons on the dN/dS values estimated by our method were observed clearly. Our method of estimation that considers the above features is a realistic representation of dN/dS values in coding sequences.

evolutionary biology↗

bioRxiv2021

Polymorphism at four-fold degenerate site, but not at the intergenic regions, explains nucleotide compositional strand asymmetry in bacteria

We investigated single nucleotide polymorphism in intergenic regions (IRs) and four-fold degenerate sites (FFS) in genomes of three {gamma}-Proteobacteria and two Firmicutes to understand the mechanism of nucleotide compositional asymmetry between the leading and the lagging strands. Pattern of the polymorphism spectra were alike regarding transitions but variable regarding transversions in the IRs of these bacteria. Contrasting trends of complementary polymorphisms such as C[->]T vs G[->]A as well as A[->]G vs T[->]C in the IRs vindicated similar replication-associated strand asymmetry regarding cytosine and adenine deamination, respectively, across these bacteria. Surprisingly, the polymorphism pattern at FFS was different from that of the IRs and its frequency was always more than the IRs in these bacteria. Further, the polymorphism patterns within a bacterium were inconsistent across the five amino acids, which neither the replication nor the transcription-associated mutations could explain. However, the polymorphism at FFS coincided with amino acid specific codon usage bias in the five bacteria. Further, strand asymmetry in nucleotide composition could be explained by the polymorphism at FFS, not at the IRs. Therefore, polymorphisms at FFS might not be treated as nearly neutral unlike that in IRs in these bacteria.

molecular biology↗