Structure and Energetics of Encapsidated DNA in Bacteriophage HK97 Studied by Scanning Calorimetry and Cryo-electron Microscopy

• Published in: Journal of molecular biology 2009-08, Vol.391 (2), p.471-483
• Main Authors: Duda, Robert L., Ross, Philip D., Cheng, Naiqian, Firek, Brian A., Hendrix, Roger W., Conway, James F., Steven, Alasdair C.
• Format: Article
• Language: English
• Subjects: 3D image reconstruction; Bacteria; Bacteriophages - chemistry; Bacteriophages - ultrastructure; Calorimetry; Calorimetry, Differential Scanning; Capsid - chemistry; Capsid - ultrastructure; Capsid Proteins - chemistry; Capsid Proteins - ultrastructure; Capsids; Condensation; conformational changes; Cryoelectron Microscopy; Denaturation; DNA; DNA condensation; DNA, Viral - chemistry; DNA, Viral - ultrastructure; Encapsidation; Enzymes; Gel electrophoresis; Genomes; head-full packaging; Heads; Ionic strength; Magnesium; mechanosensor; Melting; Microscopy; Nucleic Acid Conformation; Phage HK97; Phages; Pressure; Protein Conformation; Scanning; Shells; Signal transduction; Temperature effects; terminase; Thermal denaturation; Thermodynamics; Wounds
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2009.06.035

Encapsidation of duplex DNA by bacteriophages represents an extreme case of genome condensation, reaching near-crystalline concentrations of DNA. The HK97 system is well suited to study this phenomenon in view of the detailed knowledge of its capsid structure. To characterize the interactions involved, we combined calorimetry with cryo-electron microscopy and native gel electrophoresis. We found that, as in other phages, HK97 DNA is organized in coaxially wound nested shells. When DNA-filled capsids (heads) are scanned in buffer containing 1 mM Mg 2+, DNA melting and capsid denaturation both contribute to the complex thermal profile between 82 °C and 96 °C. In other conditions (absence of Mg 2+ and lower ionic strength), DNA melting shifts to lower temperatures and the two events are resolved. Heads release their DNA at temperatures well below the onset of DNA melting or capsid denaturation. We suggest that, on heating, the internal pressure increases, causing the DNA to exit—probably via the portal vertex–while the capsid, although largely intact, sustains local damage that leads to an earlier onset of thermal denaturation. Heads differ structurally from empty capsids in the curvature of their protein shell, a change attributable to outwards pressure exerted by the DNA. We propose that this transition is sensed by the portal that is embedded in the capsid wall, whereupon the structure of the portal and its interactions with terminase, the packaging enzyme, are altered, thus signaling that packaging is at or approaching completion.