Transcription Termination and Antitermination of Bacterial CRISPR Arrays

Abstract

A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ("repeats") interspersed with short, variable sequences ("spacers"). CRISPR arrays are transcribed and processed into individual CRISPR RNAs (crRNAs) that each include a single spacer, and direct Cas proteins to complementary sequence in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho termination functionally limits the length of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of Rho termination in the evolution of bacterial CRISPR-Cas systems.