Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of antiphage systems expression patterns is lacking. Here, we combine publicly available RNA-seq data from 14 different species with an original RNA-seq dataset of 15 Escherichia coli strains across six environmental conditions and two growth stages. Using this data, we explore the transcription patterns of 236 antiphage systems from 81 types. Defense system expression is variable along environmental, physiological, as well as spatial gradients, and can correlate with cellular physiology and mobile genetic element activity. We identify antiphage systems as cohesive but complex transcriptional units, find coordinated expression of defense islands possibly underpinned by local regulators, and demonstrate the functional relevance of differential expression in native systems. Together, these results suggest that environmental and physiological factors regulate prokaryotic immunity and may prime bacteria for infection.
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