RNA Fragments and Ribosomal Failure as a Consequence of Oxidative Stress

Researchers here describe a novel form of cell damage that results from oxidative stress, one that has not yet been investigated in any meaningful way. Oxidative stress is the name given to raised levels of oxidative molecules (free radicals, reactive oxygen species, and others) and the damage that they cause inside cells, in the form of chemical reactions that disable protein machinery. That damage is constantly occurring and constantly repaired, even in young cells, but in old cells the damage outpaces the repair mechanisms. Oxidative damage was at one time thought to be a fairly straightforward cause of aging, but that is no longer the case. It seems fairly clear nowadays that raised levels of oxidative stress in old tissues are a downstream consequence of a broad mix of other issues.

As we age, neurons in our brains can become damaged by free radicals. Researchers have discovered that this type of damage, known as oxidative stress, produces an unusual pileup of short snippets of RNA in some neurons. This RNA buildup, which the researchers believe may be a marker of neurodegenerative diseases, can reduce protein production. The researchers observed this phenomenon in both mouse and human brains, especially in a part of the brain called the striatum - a site involved in diseases such as Parkinson's and Huntington's.

For this study, the researchers used a technique that allows them to isolate and sequence messenger RNA from specific types of cells. This involves tagging ribosomes from a specific type of cells with green fluorescent protein, so that when a tissue sample is analyzed, researchers can use the fluorescent tag to isolate and sequence RNA from only those cells. This allows them to determine which proteins are being produced by different types of cells.

n separate groups of mice, the researchers tagged ribosomes from either D1 or D2 spiny projection neurons, which make up 95 percent of the neurons found in the striatum. They labeled these cells in younger mice (6 weeks old) and 2-year-old mice, which are roughly equivalent to humans in their 70s or 80s. The researchers had planned to look for gene expression differences between those two cell types, and to explore how they were affected by age. To the researchers' surprise, a mysterious result emerged - in D1 neurons from aged mice (but not neurons from young mice or D2 neurons from aged mice), they found hundreds of genes that expressed only a short fragment of the original mRNA sequence. These snippets, known as 3' untranslated regions (UTRs), were stuck to ribosomes, preventing the ribosomes from assembling normal proteins.

The 3' UTR snippets appeared to originate from about 400 genes with a wide variety of functions. Meanwhile, many other genes were totally unaffected. The researches found that the activation of oxidative stress response pathways was higher in D1 neurons compared to D2 neurons, suggesting that they are indeed undergoing more oxidative damage. The researchers propose a model for the production of isolated 3' UTRs involving an enzyme called ABCE1, which normally separates ribosomes from mRNA after translation is finished. This enzyme contains iron-sulfur clusters that can be damaged by free radicals, making it less effective at removing ribosomes, which then get stuck on the mRNA. This leads to cleavage of the RNA by a mechanism that operates upstream of stalled ribosomes.

Link: http://news.mit.edu/2018/biologists-discover-RNA-aging-neurons-1127


"It seems fairly clear nowadays that raised levels of oxidative stress in old tissues are a downstream consequence of a broad mix of other issues."

How do you know that this is a consequence and not a cause?

Posted by: Josep at November 30th, 2018 1:18 PM

@Josep: Well, where are the higher numbers of oxidative molecules coming from? About the only way to suggest they are close to a root cause is to suggest that there is some epigenetic change that causes it, and that epigenetic change is a program, not a reaction to something else. I reject that line of theory.

The proximate causes of oxidative stress are chronic inflammation, mitochondrial dysfunction, that sort of thing. Chronic inflammation is very definitely a downstream thing, from cellular senescence, but also from all sorts of other damage. Mitochondrial DNA damage in the SENS model of aging causes raised production of oxidative molecules. General mitochondrial malaise does also, and that is downstream of other issues by the look of it - like stem cell decline, a lot to do with signaling and reactions to signaling, when that signaling changes because of rising levels of molecular damage elsewhere.

Posted by: Reason at November 30th, 2018 1:33 PM

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