Thursday, July 14, 2011

E. Coli’s genetic code

Biologists report hijacking E. Coli’s genetic code
By Nicholas Wade
New York Times
July 14, 2011

Synthetic biology, the quest to hijack living systems and convert them to human-directed goals, is on the march. Last year biologists synthesized the entire genome of a small bacterium and showed how it could successfully infect a second bacterium. Now, in what may be a more significant advance, biologists have shown they can radically change a genome, not just copy it.

A team led by Farren J. Isaacs and George M. Church of the Harvard Medical School has devised a method for making hundreds of changes in a genome simultaneously. This massively parallel intervention, as the changes are known, is one of the advances that would be needed in another project Dr. Church and others have contemplated, that of recreating the mammoth by starting with an elephant’s genome and changing it at the 400,000 sites at which elephant DNA differs from that of the mammoth.

In the present instance, Dr. Isaacs and Dr. Church have been working not with a mammoth but with the standard laboratory bacterium known as E. coli. To prove they can seize control of the microbe’s genetic code and reprogram it, they have focused on one of the code’s 64 elements, known as the amber stop codon.

In Thursday’s issue of the journal Science, they report they will soon be able to delete the amber stop codon from all 314 sites in which it occurs in the E. coli genome, without harm to the organism. The codon can then be reinserted, but with a new function, like introducing a novel chemical unit into the bacterium’s proteins.

Genetic engineers have become adept at changing one gene in a genome, but it is quite another thing to alter a genome at 314 sites simultaneously.

“This is the first instance that a genome has been altered at such a large scale,” said James J. Collins, a synthetic biologist at Boston University. Along with the synthesis of a bacterial genome last year by J. Craig Venter, the advance takes synthetic biology from the gene to the genome level.

“It is a major technical breakthrough which has great promise for scientific breakthroughs to follow,” said Dr. Gerald J. Joyce, a biologist who studies the origin of life at the Scripps Research Institute in San Diego. “This is really macho molecular biotechnology.”

By taking control of the amber stop codon, Dr. Isaacs and Dr. Church have opened a door into the bacterium’s genetic programming. They could now make the bacterium incorporate a novel kind of amino acid unit into its proteins, although they have not yet done so, to Dr. Joyce’s disappointment. “They could have taken their amber codon and put in something blinky there,” he said, like a dye that would made the bacterium fluoresce.

The two leading laboratories that have taken synthetic biology to the genome level are those of Dr. Venter and Dr. Church, but their approaches are very different. Dr. Venter’s company, Synthetic Genomics, spent $40 million to make a synthetic copy of the genome of a bacterium that infects goats. Dr. Church has focused on changing an existing genome — that of the well-studied E. coli bacterium — thus avoiding the high cost of sequencing.

Dr. Church said that his approach was modular, so it can be tested at each stage, whereas Dr. Venter’s whole genome was nearly brought down by a single mutation. In contrast to Dr. Venter’s method, “our genome engineering technologies treat the chromosome as an editable and evolvable template,” Dr. Church says in his Science article.

Dr. Venter was not available for an interview, but his office issued a written comment in which he said that his goal — to design cells from scratch — could be attained only by whole-genome synthesis. He called Dr. Church’s approach, without excessive praise, “a positive addition to the field.”

Dr. Joyce of the Scripps Research Institute summed it up this way: “Craig builds the house from scratch, and George is more the remodeler, but they are both interesting houses to live in.”

The goal of synthetic biology is to take control of nature’s manufacturing system and divert it to other ends. Dr. Church’s method, which has been seven years in development, focuses on the genetic code that is common to all living things. The four different bases of DNA can be combined to make 64 three-letter words, or codons, the units in which the cell translates its genetic information into protein products.

What Dr. Church has done is to grab one of these codons for his own use by forcing the bacterium to stop using it. In future experiments he can assign this codon to other uses.

Most of the codons in the genetic code are used to designate one or another of the 20 standard amino acids of which proteins are composed. But three of the units are punctuation marks, all signaling to the cell to stop adding to a growing chain of amino acids. The chain is then released and folds up into a protein.

The E. coli bacterium uses all three stop codons, which are known as amber, ocher and umber (the first is named for Harris Bernstein, a former graduate student at the California Institute of Technology whose surname means amber in German). Dr. Church’s team converted all 314 amber stop codons in the E. coli genome to the ocher variety by changing all instances of T-A-G, in the four-letter alphabet of DNA units, to T-A-A.

The ocher stop codon works just as well as amber and, after one final step — yet to be completed — the team will have an E. coli bacterium that is not dependent on amber. They will then delete the gene whose protein recognizes the amber codon and forces a break in the protein chain. That will allow them to reinsert amber codons and, with a method devised by Peter G. Schultz of the Scripps Research Institute, reassign them to incorporate a novel amino acid into the bacterium’s proteins.

Charles R. Cantor, chief scientific officer of Sequenom, a genetic analysis and diagnostics company in San Diego, said the new method was “wonderful because it would allow expansion of the genetic code to a 21st amino acid genomewide.”

Other codons are available to be hijacked by Dr. Church’s method, and the bacterium in principle could be forced to operate an entire chemistry that was orthogonal to its own, as synthetic biologists say, meaning it had no interaction with the microbe’s natural chemistry.

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