Researchers identify key enzyme that drives the production of ribosomes

Scientists from the University of Toronto have demonstrated that an enzyme, known as RNA polymerase (Pol) II, fuels the production of the building blocks of ribosomes—the molecular machines that synthesize all cellular proteins depending on the genetic code.

(L-R) Negin Khosraviani, Karim Mekhail, and Karan (Josh) Abraham. Image Credit: University of Toronto.

This finding shows an earlier unknown role of the enzyme in the nucleolus—the site where ribosomes are produced inside the human cells and where the enzyme had not been visualized in the past. Pol II is one among the three RNA polymerases that collectively allow cells to transfer genetic data from DNA to RNA and subsequently to proteins.

Our study redefines the division of labour among the three main RNA polymerases, by identifying Pol II as a major factor in the control of nucleolar organizations underlying protein synthesis. It also provides a tool for other researchers to interrogate the function of certain nucleic acid structures more precisely across the genome.”

Karim Mekhail, Professor, Department of Laboratory Medicine and Pathobiology, University of Toronto

The study results have been recently published in the Nature journal.

Along with his collaborators, Mekhail observed that within the nucleolus, the Pol II allows the expression of ribosomal RNA gene—a crucial step in the generation of ribosomes, which are key molecular complexes that synthesize proteins in every cell.

The researchers revealed that Pol II generates hybrid DNA-RNA structures—R-loops—that immediately protect ribosomal RNA genes from molecular disruptors, known as sense intergenic non-coding RNAs, or sincRNA for short.

Such disruptors are generated by Pol I in intergenic and non-protein-coding DNA sequences between genes, and they turn out to be more active in numerous conditions: interruption of Pol II, under environmental stress, and in Ewing sarcoma.

Pol II puts the brakes on Pol I and prevents sincRNAs from ‘sinking’ the nucleolus. That’s how we united the name and action of the disruptors in our discussions of this work.”

Karim Mekhail, Professor, Department of Laboratory Medicine and Pathobiology, University of Toronto

Mekhail also holds the Canada Research Chair in Spatial Genome Organization.

Mekhail and his research group developed a novel technology to examine the role of R-loops at particular sites on chromosomes, which they named the “red laser” system.

The existing tool in the field would obliterate R-loops across the whole genome, but we wanted to test the function of R-loops associated with a given genetic locus. We were able to turn an old technology into a modern laser-guided missile, which we are still working to further improve.”

Karim Mekhail, Professor, Department of Laboratory Medicine and Pathobiology, University of Toronto

Karan (Josh) Abraham and Negin Khosraviani—two students from the University of Toronto are the co-lead authors of the study––and according to Mekhail, they made complementary and exceptional contributions to the study.

Abraham is an MD/PhD student who started to work on the study in 2014.

“I pursued this work having observed enrichment of Pol II at ribosomal DNA genes in the nucleolus, which was compelling. It’s incumbent upon every scientist to challenge existing models should the evidence support an alternate one,” stated Abraham, who will be completing his medical training next year.

Doctoral student Khosraviani joined the laboratory in 2018, and according to her, both time management and teamwork were important.

She stated, “We could not have completed this research without the help and dedication of our entire lab. Coordination with local and international collaborators was also essential.”

Mekhail’s research group worked with collaborators across the University of Toronto as well as affiliated hospitals on the research, and they also teamed up with international collaborators from the University of Miami and the University of Texas at San Antonio.

Further steps based on this study could involve investigation of sincRNAs as well as nucleolar disorganization as biomarkers for different types of cancers, and whether tumors with such characteristics react to medications that target intergenic Pol I or Pol II.

“COVID-19 has been devastating, but other diseases have not stopped,” added Mekhail, who momentarily closed his physical laboratory space during the pandemic but has continued to work with his group to examine and publish results.

“For example, cancer is still rampant and affecting people’s lives. We have to do what we can and look forward to building on the progress we’ve made as soon as possible,” Mekhail concluded.