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Developmental Biology - RNA Transcription

Going Beyond Textbook Descriptions

For the first time, researchers more clearly understand how genes are turned off and on...


New research has identified the cell process which has remained elusive to science for 50 years - despite textbook definitions. The process of turning genes off and on.
This finding is about the transcription of DNA. Transcription enables cells to make proteins and begin the work of building tissues.

During transcription, the enzyme RNA polymerase wraps around a double helix of DNA, making a copy of one of the two DNA strands. This new [3rd] strand is called RNA, and breaks off the double helix when transcription is complete. That new RNA 3rd strand now enables protein production - essential to all life - performing most of it inside cell walls.

Just as with any logical sentence, RNA needs to start and stop in the right place to make sense. A bacterial protein called Rho was discovered more than 50 years ago because of its ability to stop, or terminate, transcription. In every textbook, Rho is used as a model terminator that uses its very strong motor force to bind to RNA. But, a closer look reveals that Rho wouldn't be able to find RNAs using the textbook mechanism attributed to it.
"We started studying Rho, and realized it cannot possibly work in the way people tell us it works."

Irina Artsimovitch PhD, Professor, Microbiology, Ohio State University and co-lead author of the study.

The research, published online in the journal Science, Nov. 26, 2020, determined that instead of attaching to a specific piece of RNA near the end of transcription and helping it unwind from DNA Rho actually "hitchhikes" on RNA polymerase throughout transcription. Rho then cooperates with other proteins to eventually coax RNA through a series of structural changes that end in its inactive state enabling the final release of it as an indepedent strand.

Then using sophisticated microscopy, researchers observed how Rho acts on a transcription complex made up of RNA polymerase and two accessory proteins travelling with it throughout the transcription process.
"This is the first structure of a termination complex in any system, and was supposed to be impossible to capture because it falls apart too quickly. It answers a fundamental question: transcription is fundamental to life, and if it were not controlled, nothing would work.

RNA polymerase by itself has to be completely neutral. It has to be able to make any RNA, including those that are damaged or could harm the cell. While traveling with RNA polymerase, Rho can tell if the synthesized RNA is worth making - and if not, Rho releases it."


Irina Artsimovitch PhD

Artsimovitch has made many important discoveries about how RNA polymerase so successfully completes transcription. She didn't set out to counter years of understanding about Rho's role in termination until an undergraduate student in her lab identified surprising mutations in Rho while working on a genetics project.

Rho is known to silence expression of virulence genes in bacteria, essentially keeping them dormant until they're needed to cause infection. But, these genes do not have any RNA sequences that Rho is known to prefer binding to. Because of this, says Artsimovitch, it has never made sense that Rho looks only for specific RNA sequences, without knowing if they are still attached to RNA polymerase.

In fact, the scientific understanding of Rho's mechanism was established using simplified biochemical experiments that frequently left out RNA polymerase - in essence, defining how a process ends without factoring in the process itself.

In this work, researchers used cryo-electron microscopy to capture images of RNA polymerase operating on a DNA template in Escherichia coli, their model animal. This high-resolution visualization, combined with high-end computation, made accurate modeling of transcription termination possible.
"RNA polymerase moves along, matching hundreds of thousands of nucleotides in bacteria. The complex is extremely stable because it has to be - if RNA is released, it is lost. Yet Rho is able to make the complex fall apart in a matter of minutes, if not seconds. You can look at it, but you can't get a stable complex to analyze."

Irina Artsimovitch PhD

Using a clever method to trap complexes - just before they fall apart - scientists visualized seven complexes that represent sequential steps in the termination pathway, beginning with Rho's engagement with RNA polymerase and ending with a completely inactive RNA polymerase. The team created models and then made sure these models were correct using genetic and biochemical methods.

This study was conducted in bacteria, however, Artsimovitch believes this termination process is likely to happen in other forms of life as well.
"It appears to be common. In general, cells use similar working mechanisms from a common ancestor. They all learned [and kept] the same tricks as long as these tricks were useful."

Irina Artsimovitch PhD

Abstract
Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric ATPase on path to terminating NusA/NusG-modified elongation complexes. An open p ring contacts NusA, NusG, and multiple regions of RNA polymerase, trapping and locally unwinding proximal upstream DNA. NusA wedges into the p ring, initially sequestering RNA. Upon deflection of distal upstream DNA over the RNA polymerase Zinc-binding domain, NusA rotates underneath one capping p subunit, which subsequently captures RNA. Following detachment of NusG and clamp opening, RNA polymerase loses its grip on the RNA:DNA hybrid and is inactivated. Our structural and functional analyses suggest that p and other termination factors across life may utilize analogous strategies to allosterically trap transcription complexes in a moribund state.

Authors
Nelly Said1, Tarek Hilal, Nicholas D. Sunday, Ajay Khatri, Jorg Burger, Thorsten Mielke, Georgiy A. Belogurov, Bernhard Loll, Ranjan Sen, Irina Artsimovitch and Markus C. Wahl.


Acknowledgements
This work was supported by grants from the German Research Foundation; the German Federal Ministry of Education and Research; the Indian Council of Medical Research; the Department of Biotechnology, Government of India; the National Institutes of Health; and the Sigrid Jus?lius Foundation.

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Dec 1 2020   Fetal Timeline   Maternal Timeline   News


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RNA needs to start and stop in the correct place to assist protein production. A bacterial protein called Rho, discovered more than 50 years ago, can start or stop RNA transcription. Every textbook uses Rho as a model terminator, binding RNA. A closer look shows Rho cannot do by its textbook description. CREDIT Ohio State Univ.


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