Purine bias in bacterial genes is driven by runaway transcription

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-translation, runaway RNA polymerases that outpace trailing ribosomes have exposed nascent RNA and are vulnerable to the termination factor Rho.

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.