No abstract

Highlights d 20 Cascade complexes are required to provide 50% protection d Cascade spends equal time probing DNA (30 ms) and diffusing to a next site d Cas8e dynamically associates with Cascade in cells d CRISPR target search and invader replication compete in a kinetic ''arms race''

150) 28CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave 29 invading DNA elements. While it is thought that invaders are neutralized minutes after cell 30 entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels 31 have remained unknown. Here we visualized individual Cascade complexes in a native type I 32 CRISPR-Cas system. We uncovered an exponential relationship between Cascade copy 33 number and CRISPR interference levels, pointing to a time-driven arms race between invader 34 replication and target search, in which 20 Cascade complexes provide 50% protection. Driven 35 by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA 36 (~30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR 37 arrays affect the integrity of Cascade and impact CRISPR interference. Our work establishes 38 the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of 39 invading DNA in a crowded, DNA-packed environment. 40 41 42

Bacteriophages are an invaluable source of novel genetic diversity. Sequencing of phage genomes can reveal new proteins with potential uses as biotechnological and medical tools, and help unravel the diversity of biological mechanisms employed by phages to take over the host during viral infection. Aiming to expand the available collection of phage genomes, we have isolated, sequenced, and assembled the genome sequences of four phages that infect the clinical pathogen Klebsiella pneumoniae: vB_KpnP_FBKp16, vB_KpnP_FBKp27, vB_KpnM_FBKp34, and Jumbo phage vB_KpnM_FBKp24. The four phages show very low (0-13%) identity to genomic phage sequences deposited in the Genbank database. Three of the four phages encode tRNAs and have a GC content very dissimilar to that of the host. Importantly, the genome sequences of the phages reveal potentially novel DNA packaging mechanisms as well as distinct clades of tubulin spindle and nucleus shell proteins that some phages use to compartmentalize viral replication. Overall, this study contributes to uncovering previously unknown virus diversity, and provides novel candidates for phage therapy applications against antibiotic-resistant K. pneumoniae infections.