Researchers reveal mechanism behind RNA transcription error’s removal

25 April 2019

An international team of scientists has uncovered the mechanism used by RNA polymerase II to correct wrongly transcribed RNA nucleotides, the building units of RNA during gene transcription.

The senior researchers included Dr Peter Cheung (Butterfield Croucher Studentship 2010), Research Assistant Professor in the Department of Chemistry at Hong Kong University of Science and Technology (HKUST), along with scientists from King Abdullah University of Science and Technology in Saudi Arabia, and New York University and University of California at San Diego in the US. The team was led by HKUST’s Professor Xuhui Huang.

The building blocks of life are encoded in our DNA and through its transcription to RNA and subsequent translation of RNA to protein, proteins can perform cellular functions. Transcription is a process by which information in DNA is copied into messenger RNA, facilitated by the enzyme RNA Polymerase II.

RNA polymerase II ensures accuracy in the transcription process. First, it transcribes DNA into RNA by adding nucleotides one by one like letters in the alphabet. Then, it removes wrongly transcribed nucleotides that do not match with the DNA template to protect the cell from genetic errors that can result in cell stress or even death.

However, the precise molecular mechanism by which the enzyme executes the removal of the wrongly transcribed nucleotides had not previously been fully known.

The team used high-performance computing with computational methods to simulate the chemical reaction mediated by RNA Polymerase II to excise its target mis-incorporated nucleotides, which are composed of a nitrogenous base and a sugar molecule bound to a phosphate group.

Large-scale high-performance computing resources (provided by the Shaheen Supercomputer in collaboration with KAUST) was used to perform quantum mechanics and molecular dynamics calculations (consumed 20 million CPU core hours in total) of the RNA polymerase II system (372 atoms) to elucidate the chemical reactions of intrinsic cleavage of the mis-incorporated nucleotide (yellow). In the active site (103 atoms), the phosphate oxygen of the mis-incorporated RNA is served as the general base for the cleavage reaction without the requirement of any amino acid residues of RNA polymerase II.

“When a nucleotide is added by mistake, RNA Polymerase II can rewind by moving backwards, a process called backtracking, and cleave this mis-incorporated nucleotide,” Cheung explained.

The team discovers that the enzyme utilises an oxygen atom in the target nucleotide’s phosphate group to excise the error rather than being dependent on a specific residue in the polymerase II enzyme itself, as was initially thought.

“It is surprising to know that the enzyme can seamlessly coordinate two different chemical reactions in a single active site,” Cheung added. “While the addition of nucleotides for the synthesis of RNA depends on specific residues in RNA Polymerase II, the cleavage of the mis-incorporated nucleotides does not and is reliant on specific atoms in the mis-incorporated nucleotide. This can remarkably explain how RNA Polymerase II cleverly utilizes two distinct chemical reactions for RNA synthesis and error removal in order to coordinate the two functions effortlessly using the same active site.”

The findings, published in Nature Catalysis, offer valuable insights into how transcription may go wrong in ageing and diseased cells, and to what extent transcriptional errors may lead to various human diseases.

Dr Peter Cheung (Butterfield Croucher Studentship 2010)

Dr Peter Cheung received his Bachelor of Science degree from Queen’s University and his Master of Science from the University of Western Ontario in Canada, studying the molecular mechanism of breast cancer carcinogenesis. He received the Butterfield-Croucher scholarship in 2010 and completed his PhD degree in virology, working with influenza viruses, under the supervision of Dr Hui-Ling Yen and Professor Malik Peiris at the Center of Influenza Research. He is now a research assistant professor at the Chemistry Department at The Hong Kong University of Science and Technology, working in the transcriptional mechanisms of eukaryotes and viruses.

To view Dr Cheung’s Croucher profile, please click here