Exploring the Mechanism of Translation-Dependent Downregulation of Cas12a mRNA
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CRISPR
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Bacteria have evolved multiple defense systems, including CRISPR-Cas, to cleave the DNA of phages and mobile genetic elements (MGE). In turn, phages have evolved anti-CRISPR (Acr) proteins that use novel or co-opted mechanisms to block DNA binding or cleavage. We previously found that an anti-CRISPR protein (AcrVA2) unexpectedly inhibits Cas12a biogenesis by binding conserved and functionally important amino acids in the Cas12a N-terminal polypeptide and degrading its mRNA. However, the mechanism of Cas12a mRNA destruction remains mysterious. Here, we show that co-expressing AcrVA2 and Cas12a in a simplified in vitro transcription-translation assay does not trigger Cas12a mRNA degradation, indicating that other bacterial factors are required. We investigated whether Cas12a mRNA degradation depends on RNase E, which mediates bulk mRNA degradation as part of the degradosome. Inhibiting RNase E with the phage protein Dip (Degradosome Interacting Protein) did not affect Cas12a mRNA degradation. To search for other factors that interact with AcrVA2, we performed proximity biotinylation using AcrVA2-miniTurbo fusion proteins. We identified several interacting proteins, including ribonuclease PH, the ATP-dependent RNA helicase RhlB, Lon protease, and tRNA methyltransferase, which we will investigate in future work.