Structural basis for DNA recognition by a viral genome-packaging machine

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 121; no. 33; p. e2406138121
• Main Authors: Chechik, Maria, Greive, Sandra J., Antson, Alfred A., Jenkins, Huw T.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 13.08.2024
• Subjects: Bacteriophages - genetics; Biological Sciences; Cryoelectron Microscopy; Deoxyribonucleic acid; DNA; DNA Packaging; DNA structure; DNA viruses; DNA, Viral - chemistry; DNA, Viral - genetics; DNA, Viral - metabolism; Endodeoxyribonucleases - chemistry; Endodeoxyribonucleases - genetics; Endodeoxyribonucleases - metabolism; Genome, Viral; Genomes; Models, Molecular; Molecular modelling; Molecular structure; Nucleotide sequence; Packaging; Phages; Recognition; Terminase; Viral Genome Packaging; Virus Assembly - genetics; DNA packaging; bacteriophage HK97; virus assembly
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.2406138121

DNA recognition is critical for assembly of double-stranded DNA viruses, particularly for the initiation of packaging the viral genome into the capsid. The key component that recognizes viral DNA is the small terminase protein. Despite prior studies, the molecular mechanism for DNA recognition remained elusive. Here, we address this question by identifying the minimal site in the bacteriophage HK97 genome specifically recognized by the small terminase and determining the structure of this complex by cryoEM. The circular small terminase employs an entirely unexpected mechanism in which DNA transits through the central tunnel, and sequence-specific recognition takes place as it emerges. This recognition stems from a substructure formed by the N- and C-terminal segments of two adjacent protomers which are unstructured when DNA is absent. Such interaction ensures continuous engagement of the small terminase with DNA, enabling it to slide along the DNA while simultaneously monitoring its sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the specific cos sequence.