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Scientists Create E. Coli Bacteria With Completely Synthetic Genome

The synthetic organisms appear to function much like their natural counterparts

The synthetic DNA contains 61 codons, as opposed to the 64 typically found in living organisms (NIAID via Flickr under CC BY SA-2.0)
smithsonian.com

Researchers from England’s Medical Research Council Laboratory of Molecular Biology have successfully created E. coli bacteria with entirely human-made DNA, marking a milestone in the burgeoning field of synthetic biology and paving the way for future innovation built on so-called “designer” bacteria.

According to a new study published in the journal Nature, the synthetic genome is by far the largest of its kind. The product of a two-year research campaign, the redesigned DNA consists of four million segments—four times more than the previous record holder. Perhaps most impressively, the bacteria contain just 61 codons, as opposed to the 64 found in nearly all living creatures. Despite this seeming disparity, the synthetic bacteria appear to function much like normal E. coli. The main differences, as The New York Times’ Carl Zimmer reports, are a slower growth rate and longer length.

“It was completely unclear whether it was possible to make a genome this large and whether it was possible to change it so much,” study co-author Jason Chin, a biologist at the University of Cambridge, tells the Guardian’s Ian Sample.

But as Tom Ellis, director of the Center for Synthetic Biology at Imperial College London and a reviewer of the study, explains to Gizmodo’s Ryan Mandelbaum, the team’s efforts eventually culminated in a “tour de force” for the field: “They synthesized, built, and showed that a 4-million-base-pair synthetic genome could work,” Ellis says. “It’s more than anyone had done before.”

To “recode” a genome, scientists must manipulate the 64 codons, or three-letter combinations of the DNA molecules A, T, C and G—short for adenine, thymine, cytosine and guanine—that power all living organisms. Since each of the three positions in a codon can hold any of the four molecules, there are 64 total possible combinations (4 x 4 x 4). These combinations, in turn, correspond with specific amino acids, or organic compounds that build the proteins necessary for life. TCA, for instance, matches up with the amino acid serine, while AAG specifies lysine. TAA acts as a stop sign of sorts, signaling the organism to stop adding amino acids to a developing protein, STAT’s Sharon Begley explains.

There’s another catch to this already complex process: Since there are just 20 amino acids associated with the genetic code, multiple codons can correspond with one acid. Serine, for example, is linked with not only TCA, but AGT, AGC, TCT, TCC and TCG. As John Timmer writes for Ars Technica, the mismatch in number of codons versus amino acids makes 43 codons largely extraneous. Although cells use these extra sets as stop codes, regulatory tools and more efficient pathways toward the encoding of a specific protein, the fact remains that many are redundant.

Determining just how redundant these extra codons were took extensive trial and error. Chin tells Begley, “There are many possible ways you can recode a genome, but a lot of them are problematic: The cell dies.”

To create the successful synthetic genome, Chin and his colleagues replaced every instance of the serine codons TCG and TCA with AGC and AGT, respectively. The team also replaced every TAG codon, signaling a stop, with TAA. Ultimately, The New York Times’ Zimmer notes, the recoded DNA used four serine codons rather than four and two stop codons rather than three. Luckily, the scientists didn’t have to complete this work by hand. Instead, they made the 18,214 replacements by treating the E. coli code like an enormous text file and performing a search-and-replace function.

Transferring this synthetic DNA into the bacteria proved to be a more difficult task. Given the genome’s length and complexity, the team was unable to introduce it into a cell in one attempt; instead, the scientists approached the job in stages, painstakingly breaking the genome into pieces and transplanting it into living bacteria bit by bit.

The researchers’ accomplishment is twofold, Chin says in an interview with MIT Technology Review’s Antonio Regalado. Not only is the redesigned genome a “technical achievement,” but it also “tells you something fundamental about biology and how malleable the genetic code really is.”

According to the Guardian’s Sample, the research could help scientists create virus-resistant bacteria equipped for use in the biopharmaceutical industry; E. coli is already used to make insulin and medical compounds that treat cancer, multiple sclerosis, heart attacks and eye disease, but thanks to non-synthetic DNA’s susceptibility to certain viruses, production can be easily stalled.

Another key implication of the study centers on amino acids. As BBC News’ Roland Pease writes, the E. coli genome’s use of 61 out of 64 possible codons leaves three open for reprogramming, opening the doorway for “unnatural building blocks” capable of performing previously impossible functions.

Speaking with Zimmer, Finn Stirling, a synthetic biologist at Harvard Medical School who was not involved in the new research, concludes, “In theory, you could recode anything.”

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