Laser ‘tweezers’ unveil universal virus DNA packaging mechanism

Control of phage lambda DNA interactions: Nucleotide-dependent and independent gripping.

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Scientists used laser-powered ‘optical tweezers’ to discover a universal motor mechanism viruses use to pack their DNA into infectious particles. Published in eLife, the research is fundamental. It could change how we understand viral DNA motors and the specific roles of proteins in the motor complex. The experiments strongly support the study’s findings.

Viruses, like herpesvirus, use tiny motors fueled by ATP to pack their genetic material into shells called procapsids. Figuring out how these motors function is crucial for antiviral drug design and provides insights into cell motor mechanisms. Optical tweezers, using lasers to manipulate tiny particles, have advanced our understanding of DNA motors. They were developed by Arthur Ashkin, who won the Nobel Prize in Physics in 2018. While these tweezers help study key enzymes like terminates, questions persist about motor-DNA interactions, such as how motors grip DNA and what causes them to pause or slip.

First author Brandon Rawson, a student in the Department of Physics at the University of California San Diego, USA, said, “Studies have suggested that ATP binding causes DNA motors to grip hold of DNA, and the breakdown of ATP into ADP allows its release.“To probe this interaction in more detail, we developed a modified optical tweezer method to study the motor of a bacterial virus called phage T4, which contains a motor protein called TerL. We showed that ATP triggers TerL to grip DNA and controls the friction between the motor and DNA during slipping. In this study, we extended this to look at a motor complex containing TerL plus a lesser-understood component protein TerS to understand how they work together to control viral genome packaging.”

The team focused on the genome packaging motor of a bacterial virus similar to the one in human herpesvirus. These viruses create multiple genome copies that need separating and packaging individually. The process, called ‘unit length’ genome packaging, involves TerS starting packaging at a specific site and TerL cutting and driving the genome into a shell until another location is reached. The motor stops, TerL cuts the DNA, and the packaged particle is released.

In this study, both TerS and TerL were examined together. The team found that with both present, there was more frequent DNA gripping and high motor-DNA friction, even without ATP. This hadn’t been seen before when only TerL was present. Adding ATP or ADP increased gripping and friction, revealing two motor-DNA interaction mechanisms: nucleotide-dependent and nucleotide-independent. DNA gripping was most potent with ATP, weaker with ADP, and vulnerable without nucleotide.

In earlier studies with phage T4, the team discovered a DNA ‘end clamp’ that prevents the entire DNA from slipping out of the procapsid. This study shows that the lambda phage also uses this mechanism. Even if there’s no ATP present, if the DNA falls too much, it’s caught at the end and prevented from detaching.

Senior author Douglas Smith, UC San Diego Professor of Physics, said, “Our latest research, building on studies of viruses with different packaging methods, uncovers universal features of terminase motors. It suggests a role for the consistent TerS subunit during DNA packaging. The findings support a universal mechanism for terminase motor function driven by the TerL protein. They also highlight a key difference – more frequent DNA grip in motors with TerS, suggesting TerS acts like a sliding clamp. The separate end-clamp mechanism boosts packaging efficiency and is likely equivalent to the complex formed at the start of packaging. This implies our method could explore factors affecting the stability of this complex.”

The findings of this study contribute to a deeper understanding of viral DNA motors and highlight the conserved universal mechanism for terminase motor function, primarily driven by the TerL protein. Additionally, the study reveals a critical distinction between systems, with TerS potentially functioning as a sliding clamp and the end-clamp mechanism enhancing packaging efficiency. These insights could have significant implications for antiviral drug design and provide avenues for exploring factors affecting the stability of the motor complex.

Journal reference:

  1. Brandon Rawson, Mariam Ordyan, et al., Regulation of phage lambda packaging motor-DNA interactions: Nucleotide independent and dependent gripping and friction. eLife. DOI: 10.7554/eLife.91647.1.

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