September 1, 2015

Scientists solve another step in DNA replication puzzle

Researchers report important step in bacterial DNA replication in the prestigious journal Nature.

Imagine a traffic accident with a 20 tonne truck colliding with a small car. It can be a head-on or a rear-end collision. Does it matter which direction the car is facing, and what chance does it have of stopping the truck? 

Now let’s scale this imaginary scene down a billion-fold and on this occasion the truck moving at super high speed is the molecular machinery that copies the DNA in cells that are soon to divide and the car is a roadblock that never ever stops the truck when it is hit from behind. No surprise there! 

But when the car is hit from the front, it can stop the truck dead within a few centimetres. But it only does this half of the time. The other half of collisions result in the truck continuing without even slowing at all, as if the car wasn’t there at all. 

A team of scientists, including four researchers from UOW, have now reported in the prestigious journal, Nature, how at the molecular level in the bacteria cell the “car” (also known as the replication terminator protein Tus) stops the “truck” only when it faces in one direction, and why it does it only half of the time. 

The answer lay in a careful study of the effect of changes in the structure of Tus as it is bound to Ter, the DNA sequence it recognises. Both Tus and Ter were systematically changed in small ways and the effects on the strength of their interactions, their atomic structures, and the efficiency at which the Tus-bound blocks the DNA replication machinery were studied and correlated. This required the use of three different techniques in a collaborative effort among three research groups. 

Solving this puzzle of the ‘truck’ and ‘car’ scenario at the molecular level is another significant step in generally understanding how DNA gets replicated in cells. It’s all part of unravelling the molecular mechanisms of DNA replication and providing the fundamental knowledge required to understand disease mechanisms and antibiotic resistance. 

“We have now basically worked out how particular proteins bound to DNA can be a barrier to DNA replication and how a faster moving replication machinery can escape the blockage. This has implications for understanding of how similar blocks may form and be overcome in human cells”, according to UOW’s lead author of the paper in Nature, Professor Nick Dixon. 

“When talking about ‘trucks’ and ‘cars’ – one would expect faster moving trucks to be more efficient in crashing through the cars. 

“And that’s what we found at the molecular level too – faster moving DNA copying machines get through the ‘car’ roadblock more often than slower ones. 

Fundamental problems about how molecules work in cells has continually intrigued Professor Dixon for the past 35 years. 

“Nine years ago in a paper in Cell [2], we thought we had the answer, but there were still some unexplained aspects that continued to bug me. So I arranged to work with three collaborators with leading expertise in new technologies.

“As a result I think we now understand this intriguing problem in molecular detail as exquisite as any other mechanistic challenge in biology.”

The breakthrough was achieved using new techniques in single-molecule biochemistry developed by UOW Laureate Fellow, Professor Antoine van Oijen. A pioneer and leader in his field of research, Professor van Oijen has developed biophysical tools to study, at the level of individual molecules, important molecular processes such as DNA replication, viral fusion and membrane transport.

Professor Dixon’s UOW co-authors from the School of Chemistry and the Centre for Medical and Molecular Bioscience, Illawarra Health and Medical Research Institute, were Slobodan Jergic, Zhi-Qiang Xu and Associate Professor Aaron Oakley. The paper’s other external authors were PhD student Mohamed Elshenawy and Mohamed Sobhy, Masateru Takahashi and Samir Hamdan from the Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Saudi Arabia.