Widespread purine bias in bacterial genes driven by runaway transcription

Abstract

Genes in many bacteria are rich in purine nucleotides and poor in pyrimidines. We show that this purine preference is critical for gene expression because it prevents premature transcription termination in species that exhibit runaway transcription. In contrast to coupled transcription-translation1-5, runaway RNA polymerases that outpace trailing ribosomes have exposed nascent RNA and are vulnerable to the termination factor Rho6,7. Using a massively parallel reporter assay in Bacillus subtilis, we found that Rho-dependent termination requires a high C-to-G skew and high T content. Consequently, purine-rich coding (sense) sequences escape premature termination, whereas the correspondingly pyrimidine-rich antisense sequences are targeted by Rho and transcriptionally silenced. This purine requirement drives biased codon usage in most bacterial species with runaway transcription, except in lineages that have lost Rho. Our results suggest that the avoidance of premature transcription termination imposes major constraints on nucleotide content during genome evolution and adaptation of foreign genes.