Not so silent: mutation alters protein but not its components.

A single swap in the letters of a gene's sequence could modify the protein it encodes, even if the switch doesn't change which amino acids make up the molecule, researchers report. The finding could upset a central view in biology--that proteins made of the same amino acids are identical.

DNA contains components called nucleotides, symbolized by the letters A, T, G, and C. Each block of three of these letters--known as a codon--signals a cell's protein-making machinery to add a particular amino acid to a lengthening chain. Most of the 20 amino acids are each encoded by two or more of these three-letter combinations.

Biologists have long held that swapping one codon for another doesn't change the resulting protein's structure, as long as both codons instruct the machinery to insert the same amino acid. However, experiments by Michael Gottesman of the National Cancer Institute in Bethesda, Md., and his colleagues led the team to suspect that those silent mutations might lead to significant differences.

Gottesman's team investigates why some cancers don't respond to chemotherapy. They've found that a tiny pump, called P-glycoprotein, located on tumor cells' surfaces, can pull drugs out of cells. Some drugs are ineffective against cancer cells that have certain forms of P-glycoprotein. The researchers had noticed that individual cancer patients' pumps sometimes show differences in function, even when the pumps' proteins are made of identical combinations of amino acids.

To investigate whether silent mutations play a role, Gottesman and his colleagues worked with different varieties of the gene called MDR1, which makes P-glycoprotein. These forms of the gene contained different codons that make the same amino acids. The researchers inserted the variants into human or monkey cells that don't normally produce the pump.

Particular codon combinations affected how well the cells pumped out different cancer drugs, the researchers found. One mutant codon, called C3435T, appeared to be especially important. That codon makes the amino acid isoleucine, just as its counterpart in the most common form of the pump gene does. However, cells that had the atypical codon in combination with two other mutations in MDR1 pumped out some drugs with above-average effectiveness and others with below-average success.

Gottesman's team speculates in an upcoming Science report, published online Dec. 21, that an atypical codon may affect the pace at which cells assemble P-glycoprotein.

"If you change the speed at which a protein is made, you can end up with a slightly different final shape of the protein," says coauthor Zuben Sauna, also of the National Cancer Institute.

William Skach, who studies protein folding at Oregon Health and Science University in Portland, notes that differences in proteins that have identical amino acids "could be very widespread and not appreciated at all right now."