Archive for maio 14th, 2013

Junk-DNA: Importante Informacao sobre codigo genetico e evolucao cosmologica inserida nele

terça-feira, maio 14th, 2013

Isto precisa de uma investigacao profunda. Sugere a possibilidade de provar a tese de que o DNA-Lixo contem o registro da Evolucao Cosmologica.

New Layer of Genetic Information Discovered

(Importante notar: … which strongly supports the connection between mRNA and the corresponding protein structures and indicates that there is protein folding information in nucleic acids that is not present in the genetic code. This might give some additional explanation of codon redundancy.)


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 today 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 andMolecular 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.

What the scientists hypothesize is that the pausing exists as part of a regulatory mechanism that ensures proper checks – so that cells don’t produce proteins at the wrong time or in the wrong abundance.

A Primer on DNA Codons

All life on earth relies on the storage of genetic information in DNA (or in the case of some viruses, RNA) and the expression of that DNA into proteins to build the components of cells and carry out all life’s genetic instructions.

Every living cell in every tissue inside every organism on Earth is constantly expressing genes and translating them into proteins-from our earliest to our dying days. A significant amount of the energy we burn fuels nothing more than this fundamental process.

The genetic code is basically a universal set of instructions for translating DNA into proteins. DNA genes are composed of four types of molecules, known as bases or nucleotides (often represented by the four letters A, G, T and C). But proteins are strings of 20 different types of amino acids.

To code for all 20 amino acids, the genetic code calls for genes to be expressed by reading groups of three letters of DNA at a time for every one amino acid in a protein. These triplets of DNA letters are called codons. But because there are 64 possible ways to arrange three bases of DNA together – and only 20 amino acids used by life – the number of codons exceeds the demand. So several of these 64 codons code for the same amino acid.

Scientists have known about this redundancy for 50 years, but in recent years, as more and more genomes from creatures as diverse as domestic dogs to wild rice have been decoded, scientists have come to appreciate that not all redundant codons are equal.

Many organisms have a clear preference for one type of codon over another, even though the end result is the same. This begged the question the new research answered: if redundant codons do the same thing, why would nature prefer one to the other?

The article, “The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria,” by Gene-Wei Li, Eugene Oh, and Jonathan S. Weissman, was published by the journal Nature on March 28.


NATURE – Artigo so pode ver o abstracto.

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

Nature -484, 538–541 doi:10.1038/nature10965 – Published online – 28 March 2012

 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 fragments345. 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 ribosome78 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


The Shine-Dalgarno sequence (or Shine-Dalgarno box), proposed by Australian scientists John Shine (b.1946) and Lynn Dalgarno (b.1935),[1] is a ribosomal binding site in the mRNA, generally located 8 bases upstream of the start codon AUG. The Shine-Dalgarno sequence exists both in bacteria and archaea, being also present in some chloroplastic and mitochondial transcripts. The six-base consensus sequence is AGGAGG; in E. coli, for example, the sequence is AGGAGGU. This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon. The complementary sequence (UCCUCC), is called the anti-Shine-Dalgarno sequence and is located at the 3′ end of the 16S rRNA in the ribosome. The eukaryotic equivalent of the Shine-Dalgarno sequence is called the Kozak sequence.

Mutations in the Shine-Dalgarno sequence can reduce translation. This reduction is due to a reduced mRNA-ribosome pairing efficiency, as evidenced by the fact that complementary mutations in the anti-Shine-Dalgarno sequence can restore translation.

The Shine-Dalgarno sequence GAGG dominates in bacteriophage T4 early genes, whereas the sequence GGAG is a target for the T4 endonuclease RegB that initiates the early mRNA degradation.[2]

When the Shine-Dalgarno sequence and anti-Shine-Dalgarno sequence pair, the translation initiation factors IF2-GTPIF1IF3, as well as the initiator tRNA fMet-tRNA(fmet) are recruited to the ribosome.

The ribosomal S1 protein in Gram-negative bacteria [edit]

In Gram-negative bacteria, the presence of a Shine-Dalgarno sequence is not obligatory for the ribosome to locate the initiator codon. Numerous prokaryotic mRNAs don’t possess Shine-Dalgarno sequences at all: ribosomal protein S1, which binds to AU-rich sequences found in many prokaryotic mRNAs 15-30 nucleotides upstream of start-codon, can instigate translation initiation in the case of these mRNAs.

SD-Sequences in Chloroplasts [edit]

Although plastids are prokaryotic descendants and still have their prokaryotic translational machinery, SD-like sequences are not required at least in green alga Chlamydomonas reinhardtiichloroplasts according to a study.[3]

See also [edit]

The Kozak consensus sequenceKozak consensus or Kozak sequence, is a sequence which occurs on eukaryotic mRNA and has the consensus (gcc)gccRccAUGG. The Kozak consensus sequence plays a major role in the initiation of the translation process.[1] The sequence was named after the person who brought it to prominence, Marilyn Kozak.

The sequence is identified by the notation (gcc)gccRccAUGG, which summarizes data analysed by Kozak from a wide variety of sources (about 699 in all)[2] as follows:

  1. a lower case letter denotes the most common base at a position where the base can nevertheless vary;
  2. upper case letters indicate highly-conserved bases, i.e. the ‘AUGG’ sequence is constant or rarely, if ever, changes, with the exception being the IUPAC ambiguity code [3] ‘R’ which indicates that a purine (adenine or guanine) is always observed at this position (with adenine being claimed by Kozak to be more frequent); and
  3. the sequence in brackets ((gcc)) is of uncertain significance.
Como a Matrix une evolucao do macrotempo cosmologico com o microtempo biologico no DNA

Como a Matrix une evolucao do macrotempo cosmologico com o microtempo biologico no DNA

Kozak’s paper was limited to a subset of vertebrates (i.e. human, cow, cat, dog, chicken, guinea pig, hamster, mouse, pig, rabbit, sheep, and xenopus)


Original Paper em PDF

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

Gene-Wei Li1 – , Eugene Oh1 & Jonathan S. Weissman1

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

– 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 SDlike sequences are a major determinant of translation rates and global driving force for the coding of bacterial genomes.

established that different mRNAs could be translated with different elongation rates

– there was a clear correspondence on individual transcripts between SD-like sequences and pauses.


Editor’s summary

Keeping protein synthesis on track

The rate of protein synthesis by the ribosome can be influenced by various intrinsic and extrinsic factors, such as structure in the messenger RNA and the actions of RNA binding proteins. As a result, translation is subject to transient pausing. This study provides a genome-wide view of the locations of ribosome pausing in bacteria. The most common origin of pausing is found to be hybridization between the ribosomal RNA and internal sequences of the mRNA that are similar to the Shine–Dalgarno element that serves as the entry point for the ribosome. To prevent their interference with translation, such Shine–Dalgarno-like elements are underrepresented in protein-coding sequences, accounting for some of the observed bias in codon usage. These results have implications both for our basic understanding of protein synthesis and for practical efforts to express recombinant proteins.