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Old 29th March 2012, 05:45 PM
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Default Genetic Information Helps Determine How Fast Proteins Are Produced

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New Layer of Genetic Information Helps Determine How Fast Proteins Are Produced


The structure of a ribosome (Credit: Image courtesy of University of California - San Francisco)

ScienceDaily (Mar. 28, 2012) — A hidden and never before recognized layer of information in the genetic code has been uncovered by a team of scientists at the University of California, San Francisco (UCSF) thanks to a technique developed at UCSF called ribosome profiling, which enables the measurement of gene activity inside living cells -- including the speed with which proteins are made.
By measuring the rate of protein production in bacteria, the team discovered that slight genetic alterations could have a dramatic effect. This was true even for seemingly insignificant genetic changes known as "silent mutations," which swap out a single DNA letter without changing the ultimate gene product. To their surprise, the scientists found these changes can slow the protein production process to one-tenth of its normal speed or less.
As described March 28 in the journal Nature, the speed change is caused by information contained in what are known as redundant codons -- small pieces of DNA that form part of the genetic code. They were called "redundant" because they were previously thought to contain duplicative rather than unique instructions.
This new discovery challenges half a century of fundamental assumptions in biology. It may also help speed up the industrial production of proteins, which is crucial for making biofuels and biological drugs used to treat many common diseases, ranging from diabetes to cancer.
"The genetic code has been thought to be redundant, but redundant codons are clearly not identical," said Jonathan Weissman, PhD, a Howard Hughes Medical Institute Investigator in the UCSF School of Medicine Department of Cellular and Molecular Pharmacology.
"We didn't understand much about the rules," he added, but the new work suggests nature selects among redundant codons based on genetic speed as well as genetic meaning.
Similarly, a person texting a message to a friend might opt to type, "NP" instead of "No problem." They both mean the same thing, but one is faster to thumb than the other.
How Ribosome Profiling Works
The work addresses an observation scientists have long made that the process protein synthesis, so essential to all living organisms on Earth, is not smooth and uniform, but rather proceeds in fits and starts. Some unknown mechanism seemed to control the speed with which proteins are made, but nobody knew what it was.
To find out, Weissman and UCSF postdoctoral researcher Gene-Wei Li, PhD, drew upon a broader past effort by Weissman and his colleagues to develop a novel laboratory technique called "ribosome profiling," which allows scientists to examine universally which genes are active in a cell and how fast they are being translated into proteins.
Ribosome profiling takes account of gene activity by pilfering from a cell all the molecular machines known as ribosomes. Typical bacterial cells are filled with hundreds of thousands of these ribosomes, and human cells have even more. They play a key role in life by translating genetic messages into proteins. Isolating them and pulling out all their genetic material allows scientists to see what proteins a cell is making and where they are in the process.
Weissman and Li were able to use this technique to measure the rate of protein synthesis by looking statistically at all the genes being expressed in a bacterial cell.
They found that proteins made from genes containing particular sequences (referred to technically as Shine-Dalgarno sequences) were produced more slowly than identical proteins made from genes with different but redundant codons. They showed that they could introduce pauses into protein production by introducing such sequences into genes.
More here:-

http://www.sciencedaily.com/releases...0328142850.htm

Source [abstract only]:-

Li, G.-W., E. Oh, et al. (2012). "The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria." Nature advance online publication.
Quote:
Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding1. These pauses are influenced by the sequence of the messenger RNA2. Thus, redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria by ribosome profiling—deep sequencing of ribosome-protected mRNA fragments3, 4, 5. This approach enables the high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare transfer RNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine–Dalgarno-(SD)6-like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome7, 8 possessing an altered anti-SD sequence, we show that pausing is due to hybridization between the mRNA and 16S ribosomal RNA of the translating ribosome. In protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes.
http://www.nature.com/nature/journal...ture10965.html
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