Two star labs (the Zhang lab, the Sternburg lab) recently published two back-to-back papers that reveal a novel phage-defense mechanism in Klebsiella pneumoniae.

The studies showed that phage-defending proteins are synthesized in the bacteria, not through the traditional DNA to mRNA, and, to the effector proteins (i.e., restriction enzyme, Cas nuclease). Instead, the bacteria encode about a 120-base short piece of non-coding RNA (ncRNA), which is used as a template for making a very long, repetitive single-strand cDNA template through rolling circle reverse transcription activity. Upon phage infection, the cDNA is activated into a double-stranded form and produces toxic proteins to arrest bacterial growth, thus preventing phage propagation.

This RT-based phage-defense system is called DRT2 (defense-associated RT2). If we think about RTs in bacteria, it can incorporate viral DNA into CRISPR spacers. RT in retron also synthesizes specialized RNA/DNA/protein complexes for phage defense. It seems like RT is often involved in phage defense. So, that is why the authors in these two groups are specifically looking into bacterial reverse transcription.

I really like the short review article article on Science about these two papers. It is titled “Tricking phages with a reverse move”. Initially, I could not understand what does this mean. As I read through it, I had this “aha moment” where I realized bacteria are indeed smart to develop this system for phage defense. The ncRNA and the inactivated cDNA template are pre-made before phages even appear. Such cDNA repeats of sequences are called neo (near-endless ORF) in both studies (likely not due to coincidence) and no repressor and the toxin effector protein just keeps being made for bacterial suicide.

Viruses (i.e., Mu phage) like plasmids and transposons can move within or cross-genome. Cells have an innate resistance to mobile genomic elements (MGEs) because uncontrolled genome shuffling can lead to genomic instability and chaos. The transposable bacteriophage, in some sense, is an active MGE for the bacterial host. It inserts almost anywhere in the chromosome and trashes the host genome during the lytic pathway in phage infection.

“MGEs themselves often provide the source material from which anti-MGE mechanisms are derived.” (Tang et al., Science 2024)

The prominent example in bacteria is that the CRISPR phage defense system could be derived from CRISPR-like transposons, which both have RNA-guided nuclease activities.