Genomic and mechanistic insights of convergent transcription in bacterial genomes

Abstract

Convergent gene pairs with overlapping head-to-head configuration are widely spread across both eukaryotic and prokaryotic genomes. They are believed to contribute to the regulation of genes at both transcriptional and post-transcriptional levels, although the factors contributing to their abundance across genomes and mechanistic basis for their prevalence are poorly understood. In this study, we explore the role of various factors contributing to convergent overlapping transcription in bacterial genomes. Our analysis shows that the proportion of convergent overlapping gene pairs (COGPs) in a genome is affected by endospore formation, bacterial habitat and the temperature range. In particular, we show that bacterial genomes thriving in specialized habitats such as thermophiles exhibit a high proportion of COGPs. Our results also show that the density distribution of COGPs across the genomes is high for shorter overlaps with increased conservation of distances for decreasing overlaps. Our study also reveals that COGPs frequently contain stop codon overlaps with the middle base exhibiting mismatches between complementary strands. Functional analysis using COGs (Cluster of Orthologous groups) annotations suggested that cell motility, cell metabolism, storage, and cell signaling are enriched among COGPs suggesting their role in processes beyond regulation. Our analysis provides genomic insights into this unappreciated regulatory phenomenon, allowing a refined understanding of their contribution to bacterial phenotypes.