For the first time, researchers describe how Rho protein really stops gene expression.
New research has identified and described a cellular process that, despite what textbooks say, has remained elusive to scientists until now — precisely how the copying of genetic material that, once started, is properly turned off.
The finding concerns a key process essential to life: the transcription phase of gene expression, which enables cells to live and do their jobs.
During transcription, an enzyme called RNA polymerase wraps itself around the double helix of DNA, using one strand to match nucleotides to make a copy of genetic material — resulting in a newly synthesized strand of RNA that breaks off when transcription is complete. That RNA enables the production of proteins, which are essential to all life and perform most of the work inside cells.
Just as with any coherent message, 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, using its very strong motor force, binds to the RNA and pulls it out of RNA polymerase. But a closer look by these scientists showed that Rho wouldn’t be able to find the RNAs it needs to release using the textbook mechanism.
“We started studying Rho, and realized it cannot possibly work in ways people tell us it works,” said Irina Artsimovitch, co-lead author of the study and professor of microbiology at The Ohio State University.
The research, published online by the journal Science today, November 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 for the duration of transcription. Rho cooperates with other proteins to eventually coax the enzyme through a series of structural changes that end with an inactive state enabling release of the RNA.
The team used sophisticated microscopes to reveal how Rho acts on a complete transcription complex composed of RNA polymerase and two accessory proteins that travel with it throughout transcription.
“This is the first structure of a termination complex in any system, and was supposed to be impossible to obtain because it falls apart too quickly,” Artsimovitch said.
“It answers a fundamental question — transcription is fundamental to life, but 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.”
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 the 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 preferentially bind. Because of that, Artsimovitch said, it has never made sense that Rho looks only for specific RNA sequences, without even knowing if they are still attached to RNA polymerase.
In fact, the scientific understanding of the Rho 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, the researchers used cryo-electron microscopy to capture images of RNA polymerase operating on a DNA template in Escherichia coli, their model system. 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 the RNA is released, it is lost,” Artsimovitch said. “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.”
Using a clever method to trap complexes just before they fall apart enabled the scientists to visualize seven complexes that represent sequential steps in the termination pathway, starting from Rho’s engagement with RNA polymerase and ending with a completely inactive RNA polymerase. The team created models based on what they saw, and then made sure that these models were correct using genetic and biochemical methods.
Though the study was conducted in bacteria, Artsimovitch said this termination process is likely to occur in other forms of life.
“It appears to be common,” she said. “In general, cells use similar working mechanisms from a common ancestor. They all learned the same tricks as long as these tricks were useful.”
Reference: “Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ” by Nelly Said, Tarek Hilal, Nicholas D. Sunday, Ajay Khatri, Jörg Bürger, Thorsten Mielke, Georgiy A. Belogurov, Bernhard Loll, Ranjan Sen, Irina Artsimovitch and Markus C. Wahl, 26 November 2020, Science.
DOI: 10.1126/science.abd1673
Artsimovitch, working with an international research team of collaborators, co-led the study with Markus Wahl, a former Ohio State graduate student now at Freie Universität Berlin.
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 Jusélius Foundation.
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3 Comments
Babu G. Ranganathan*
(B.A. Bible/Biology)
THE CELL could not have evolved. A partially evolved cell would quickly disintegrate under the effects of random forces of the environment, especially without the protection of a complete and fully functioning cell membrane. A partially evolved cell cannot wait millions of years for chance to make it complete and living! In fact, it couldn’t have even reached the partially evolved state.
CATCH-22 FOR EVOLUTIONARY ORIGIN OF LIFE
Just having the right materials, elements, and conditions do not mean that life can arise by chance.
Miller, in his famous experiment in 1953 showed that individual amino acids (the building blocks of life) could come into existence by chance. But, it’s not enough just to have amino acids. The various amino acids that make-up life must link together in a precise sequence, just like the letters in a sentence, to form functioning protein molecules. If they’re not in the right sequence the protein molecules won’t work. It has never been shown that various amino acids can bind together into a sequence by chance to form protein molecules. Even the simplest cell is made up of many millions of various protein molecules.
What many don’t realize is that although oxygen is necessary for life’s processes, the presence of oxygen would prevent life from coming into being. This is because oxygen is destructive unless there are mechanisms already in place to control, direct, and regulate it, such as what we find in already existing forms of life.
RNA and DNA are made up of molecules (nucleic acids) that must also exist in the right sequence. Furthermore, none of these sequential molecules, proteins, DNA, RNA, can function outside of a complete and living cell and all are mutually dependent on one another. One cannot come into existence without the other.
Mathematicians have said any event in the universe with odds of 10 to 50th power or greater is impossible! The probability of just a single average size protein molecule arising by chance is 10 to the 65th power. The late great British scientist Sir Frederick Hoyle calculated that the odds of even the simplest cell coming into existence by chance is 10 to the 40,000th power! How large is this? Consider that the total number of atoms in our universe is 10 to the 82nd power.
The cell could not have evolved. A partially evolved cell would quickly disintegrate under the effects of random forces of the environment, especially without the protection of a complete and fully functioning cell membrane. A partially evolved cell cannot wait millions of years for chance to make it complete and living! In fact, it couldn’t have even reached the partially evolved state.
Alien beings, even if they do exist, could not have evolved. How could they have survived millions of years while the very biological structures, organs, and systems necessary for their survival were supposedly still evolving? Life, in any form (even a single-celled organism), must be complete, fully integrated, and fully-functioning from the very start to be fit for survival.
Of course, once there is a complete and living cell then the code and mechanisms exist to direct the formation of more cells. The problem for evolutionists is how did the cell originate when there were no directing code and mechanisms in nature. Natural laws may explain how a cell or airplane works but mere undirected natural laws could not have brought about the existence of either.
What about synthetic life? Scientists didn’t create life itself. What they’ve done is, by using intelligent design and sophisticated technology, scientists built DNA code from scratch and then they implanted that man-made DNA into an already existing living cell and alter that cell. That’s what synthetic life is.
Through genetic engineering scientists have been able to produce new forms of life by altering already existing forms of life, but they have never created life from non-living matter. Even if they do, it won’t be by chance but by intelligent design. That doesn’t help the theory of evolution.
What about natural selection? Natural selection doesn’t create or produce anything. It can only “select” from biological variations that are possible and which have survival value. If a variation occurs that helps a species survive, that survival is called ” natural selection.” It’s a passive process. There’s no conscious selection by nature, and natural selection only operates in nature once there is life and reproduction and not before, so it would not be of assistance to the origin of life.
Science can’t prove we’re here by chance or design. Neither was observed. Both are positions of faith. The issue is which faith is best supported by science. Let the scientific arguments of both sides be presented.
Read my popular Internet articles:
THE NATURAL LIMITS TO EVOLUTION
ANY LIFE ON MARS CAME FROM EARTH
Visit my Internet site: THE SCIENCE SUPPORTING CREATION
Author of the popular Internet article, TRADITIONAL DOCTRINE OF HELL EVOLVED FROM GREEK ROOTS
*I have given successful lectures (with question and answer period afterwards) defending creation before evolutionist science faculty and students at various colleges and universities. I’ve been privileged to be recognized in the 24th edition of Marquis “Who’s Who in The East” for my writings on religion and science.
There’s also the ‘handedness’ in the Urey – Miller/ Miller – Urey outcome.
Also:
This is troubling in the thankless and sinister world of information domination cruelties by governments and the elitist government classes.
Most advocates for Intelligent Design/Creationism serm to possess a strong psychological aversion to uncertainty plus a dogmatically limited imagination. Not a lack of imagination, per se, but rather an active unwillingness to seriously entertain the very real possibility that answers not yet discovered are also unattainable, so they default to paradigms and “answers” provided under the Color of Authority, specifically Scriptural authority.
Since the beginning of the Scientific Revolution and the Age of Enlightenment, numerous natural phenomena have been shown to have perfectly plausible explanations that rely only upon natural processes (i.e., without divine intervention). Biological Life is astoundingly complex. It is simplistic to assume that complete chemical descriptions of the intermediate steps in all life processes would not also be astoundingly complex.
DNA and chromosomes as carriers of genetic information was only confirmed last century. Our technologies for interrogating the details of peptide and protein synthesis have only matured to reveal fine details during the last fifty years, and especially the last 25 years. Metaphorically, we are “children” just mastering how to “read” the minute details of intracellular biochemical processes. There is every reason to believe that as our sophistication in interrogating and understanding these processes improves, question that currently seem beyond our comprehension will be answered with clear yet highly complex “mechanistic” answers. No hand waving or deux ex machina needed. And that possibility terrifies many religious believers, because ~if~ all life can be explained without the metaphorical “watchmaker”, then, perhaps, the cited Watchmaker ~may not~ exist, calling into question all ancillary claims about a non-corporeal essence and the persistence of consciousness separate from a living brain.
I am neither an anti-theist nor an evangelical theist. Both perspectives seem plausible. But the *possibility* of something and the fact of something ate not direct correlates. Where the interaction of matter and energy, including biochemistry, ate concerned, Science serms abundantly capable of delivering answers …eventually. I believe Einstein is attributed with the quote: “Nature is subtle, but it is not deceptive.”
Regarding the likelihood the first cells emerged from inanimate chemistry, I am reminded of Warren Buffet’s observation regarding investing: “Not every investment will be a ‘winner’, but it only takes one successful investment to return amazing returns!”
Nature had *at least* 100’s of millions of years to throw together untold variations of chemical possibilities. many likely “worked” ~somewhat~, and many may have amalgamated in various admixtures until one was stable and self-replicating. Once that single example stabilized. Random mutation and “fitness” to environmental stressors pushed biological evolution forward. Early Earth’s atmosphere was largely anoxic. The emergence of chlorophyll and photosynthesis led to a gradual increase in atmospheric oxygen levels. Once a prokaryote engulfed the predecessor to mitochondria, the next great leap was rooted.
No magis required, just the slow steady process of mutation and adaption over billions of years.
Some humans ate simply too impatient to imagine anything worthwhile actually iterating over such great lengths of time.