Antisense RNA controls the degradation of phycobilisomes in heterocyst-forming cyanobacteria by a transcriptional interference mechanism.

Transcriptional interference is rarely documented in bacteria. In cyanobacteria, phycobilisomes are the major light-harvesting antennae, and their degradation under non-optimal conditions follows a tightly regulated genetic program leading to the production of NblA, a widely conserved proteolytic adapter. NblA production is regulated at both the transcriptional and post-transcriptional levels. Here, we uncover an additional regulatory layer mediated by an antisense RNA conserved in heterocyst-forming cyanobacteria. In Nostoc sp. PCC 7120, transcription of the abundant antisense RNA (as_nblA) limits nblA mRNA accumulation. A strain unable to transcribe as_nblA produces an excess of NblA, ultimately so harmful that suppressor mutations of nblA expression accumulate rapidly, underscoring the essential role of as_nblA. Rifampicin time-series experiments and the inability of as_nblA to regulate nblA expression in trans support transcriptional interference as the primary regulatory mechanism of as_nblA. Mathematical modeling of nblA expression, supported by biological data, shows that as_nblA plays a pivotal role in preventing leaky nblA expression under non-inducing conditions. Our work highlights the importance of antisense RNA-mediated regulation, particularly transcriptional interference, in establishing thresholds that prevent spurious expression of genes encoding critical cellular functions.