On the Road to Protein: RNA Escapes Nucleus

Image by Biology Big Brother

[Image by Biology Big Brother]

A breakthrough — published in the September 15 online edition of Nature —  explains at last the mystery at the heart of the central dogma of molecular biology.

In 1958, climbing the double helix stairway to a Nobel Prize, Francis Crick explained (and elaborated in 1970) what we now call “The central dogma of molecular biology” that is the backbone of the theory of information in the nucleus of living cells. It states that information can’t be transferred back from protein to either protein or nucleic acid, because the normal flow of biological information has three steps:
(1) DNA information is copied to DNA (called replication),
(2) DNA information is copied into mRNA, (called transcription), and
(3) proteins are synthesized from mRNA information (called translation).

He even used the word dogma, as explained in his 1988 autobiography, What Mad Pursuit:

I called this idea the central dogma, for two reasons, I suspect. I had already used the obvious word hypothesis in the sequence hypothesis, and in addition I wanted to suggest that this new assumption was more central and more powerful. … As it turned out, the use of the word dogma caused almost more trouble than it was worth. … Many years later Jacques Monod pointed out to me that I did not appear to understand the correct use of the word dogma, which is a belief that cannot be doubted. I did apprehend this in a vague sort of way but since I thought that all religious beliefs were without foundation, I used the word the way I myself thought about it, not as most of the world does, and simply applied it to a grand hypothesis that, however plausible, had little direct experimental support.

Horace Freeland Judson quotes Crick in a 1996 biography, The Eighth Day of Creation: “‘My mind was, that a dogma was an idea for which there was no reasonable evidence. You see?!’ And Crick gave a roar of delight. “I just didn’t know what dogma meant. And I could just as well have called it the ‘Central Hypothesis,’ or — you know. Which is what I meant to say. Dogma was just a catch phrase.’”

The central dogma of molecular biology has a loophole, critical to the HIV virus, called “reverse transcriptase” — a molecule discovered by David Baltimore in 1970 at MIT, and independently by Howard Temin at the University of Wisconsin–Madison. The two shared the 1975 Nobel Prize in Physiology or Medicine with Renato Dulbecco for the discovery that some viruses use reverse transcriptase to create single-stranded DNA from an RNA template, which is information driving against the flow of traffic on the Central Dogma freeway.

But even within the central dogma of molecular biology, a mystery has lingered for half a century.  How does RNA escape the cell’s nucleus and travel out into the cytoplasm where it can be used to direct the manufacture of proteins?

Protein synthesis may be the highest priority cellular process. Data for making proteins are encoded in the DNA (Deoxyribonucleic acid) of genes, coiled and folded into chromosomes in the cell’s nucleus. To perform protein synthesis, and make the dominant molecules of your body, DNA data are copied (transcribed) onto messenger RNA.  But here’s the catch: these molecules of messenger RNA must then travel from the nucleus, through a double barrier, and into the cytoplasm, where amino acids get linked together like a strand of pearls to become the specified proteins.

The double barrier is variously called the nuclear envelope or the nuclear membrane.  It consists of an inner and an outer membrane, arranged parallel to one another and separated by 10 to 50 nm (nanometers, billionths of a meter). This completely encloses the nucleus and separates the cell’s genetic material from the surrounding cytoplasm. The nuclear membrane prevents macromolecules from diffusing freely just as inner and outer walls of a prison might allow air in and out, but not inmates.  So how does the RNA get out where it can do its job?

Before a recent breakthrough [“How Molecules Escape from Cell’s Nucleus: Key Advance in Using Microscopy to Reveal Secrets of Living Cells”, Science Daily,] the limit of microscopy resolution was 200 nanometers.  Molecules in living cells closer together could not be distinguished as separate entities. Indirect evidence suggested that RNA molecules translocated — got through portholes called nuclear pores.  But nobody had ever seen this in action. We needed a super-microscope.

Robert Singer, Ph.D., and colleagues to the rescue.  Singer (Professor and Co-Chair of Anatomy and Structural Biology, Professor of Cell Biology and Neuroscience and co-director of the Gruss-Lipper Biophotonics Center at Albert Einstein College of Medicine of Yeshiva University) is the senior author of the new study. These researchers improved the resolution limit by a factor of 10, successfully differentiating molecules only 20 nanometers apart. What did they see?

“Up until now, we’d really had no idea how messenger RNA travels through nuclear pores,” said Dr. Singer. “Researchers intuitively thought that the squeezing of these molecules through a narrow channel such as the nuclear pore would be the slow part of the translocation process. But to our surprise, we observed that messenger RNA molecules pass rapidly through the nuclear pores, and that the slow events were docking on the nuclear side and then waiting for release into the cytoplasm.”

But wait, there’s more.  Dr. Robert Singer observed that single messenger RNA molecules arrive at the nuclear pore and then wait for 80 milliseconds (80 thousandths of a second) to enter.  Then they zoom through the pore remarkably fast — in just 5 milliseconds.  For the next step, the molecules wait on the outside (cytoplasm side) of the pore for another 80 milliseconds before being released. This specific timing, plus measurements showing that 10 percent of messenger RNA molecules pause for seconds at nuclear pores without gaining entry, indicates that messenger RNA could be screened for quality at this point.

Dr. Singer: “Researchers have speculated that messenger RNA molecules that are defective in some way, perhaps because the genes they’re derived from are mutated, may be inspected and destroyed before getting into the cytoplasm or a short time later, and the question has been, ‘Where might that surveillance be happening?  So we’re wondering if those messenger RNA molecules that couldn’t get through the nuclear pores were subjected to a quality control mechanism that didn’t give them a clean bill of health for entry.”

This might lead to a huge leap towards in curing a terrible disease,myotonic dystrophy, just as previous deconstruction of the centraldogma and insights into RNA dynamics led to medical advances thatcombat AIDS. In the case of AIDS, studies showed that the retroviruses take informationfrom RNA and copy them to DNA, instead of the usual direction ofinformation flow.  In the case of myotonic dystrophy, we may in thenear future have a way to get messenger RNA that had been stuck inthe nucleus and unable to enter the cytoplasm through the pores. This would be done bymodifying the pores; the timing of nucleocytoplasmic transport throughthe pores; or creating an alternative way to get the mRNA where it is needed tosynthesize proteins and make the patient healthy

Dr. Singer had earlier in his career studied myotonic dystrophy, which is a severe inherited disorder marked by wasting of the muscles and caused by a mutation involving repeated DNA sequences of three nucleotides. Dr. Singer had noted that in the cells of people with myotonic dystrophy, messenger RNA gets stuck in the nucleus and cannot enter the cytoplasm. “By understanding how messenger RNA exits the nucleus, we may be able to develop treatments for myotonic dystrophy and other disorders in which messenger RNA transport is blocked,” he said.

Half a century of investigating the central dogma of molecular biology has brought us closer to a cure for AIDS.  Now a new super-microscope, and a dedicated team of medical scientists, may have new approaches to reducing human suffering.

On the road to synthesizing protein, we’ve seen the jailbreak of RNA escaping the nucleus.


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