ScienceDaily (July 3, 2012) oxic chemicals wreak havoc on cells, damaging DNA and other critical molecules. A new study from researchers at MIT and the University at Albany reveals how a molecular emergency-response system shifts the cell into damage-control mode and helps it survive such attacks by rapidly producing proteins that counteract the harm.

Peter Dedon, a professor of biological engineering at MIT, and colleagues had previously shown that cells treated with poisons such as arsenic alter their chemical modification of molecules known as transfer RNA (tRNA), which deliver protein building blocks within a cell. In their new paper, appearing in the July 3 issue of Nature Communications, the research team delved into how these modifications help cells survive.

The researchers found that toxic stresses reprogram the tRNA modifications to turn on a system that diverts the cell's protein-building machinery away from its routine activities to emergency action. "In the end, a stepwise mechanism leads to selective expression of proteins that you need to survive," says Dedon, senior author of the Nature Communications paper.

The findings offer insight into not only cells' response to toxins, but also their reactions to all kinds of stimuli, such as nutrients or hormones, Dedon says. "We're proposing that any time there's a stimulus, you're going to have a reprogramming [of tRNA] that causes selective translation of proteins you need for the next step in whatever you're going to do," he says.

Lead author of the paper is recent MIT PhD recipient Clement Chan. Other MIT authors are postdocs Yan Ling Joy Pang and Wenjun Deng and research scientist Ramesh Indrakanti. Authors from the University at Albany are Thomas Begley, an associate professor of nanobioscience, and research scientist Madhu Dyavaiah.

A new role for RNA

Transfer RNA is made of 70 to 90 ribonucleotide building blocks. After synthesis, the ribonucleotides usually undergo dozens of chemical modifications that alter their structure and function. The primary job of tRNA is to bring amino acids to the ribosomes, which string them together to make proteins.

In a 2010 paper, Dedon and colleagues exposed yeast cells to different toxic chemicals, including hydrogen peroxide, bleach and arsenic. In each case, the cells responded by uniquely reprogramming the location and amount of each tRNA modification. If the cells lost the ability to reprogram the modifications, they were much less likely to survive the toxic attack.

In the new study, the researchers focused on a particular tRNA modification, known as m5C, which occurs when cells encounter hydrogen peroxide, a chemical produced by white blood cells.

They first discovered that this modification occurs predominantly in one of the tRNAs that carry the amino acid leucine. Every amino acid is encoded by three-letter sequences in the genome called codons. Each tRNA corresponds to one amino acid, but most amino acids can be coded by several tRNA sequences. For example, leucine can be coded by six different genome sequences: TTA, TTG, CTT, CTC, CTA and CTG.

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Genetic 911: Cells' emergency systems revealed