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especially among bacteria, which can be as different from one another as humans are from oak trees. 20 This is why gene transfer is so powerful, and the most important reason why bacteria are masters of metabolic innovation. Very different organisms harbor very different metabolic texts, and gene transfer can edit one text with borrowed passages that are very different yet meaningful within another text, the microbial equivalent of a musical mash-up that combines a Baroque instrumental track with a pop vocal. Only some edits will improve a text, because the recipient cannot pick and choose which new genes it gets—they are a random subset of the donor’s genome. But because gene transfer is incredibly frequent, the odds for innovation aren’t bad: Even though many edits lack luster, the shelves of life’s universal library contain a virtually infinite number of masterpieces waiting to be found.
An example of nature’s editorial prowess is our friend
E. coli
and its multiple varieties,
E. coli
strains that were long thought to be like closely related ethnic groups. 21 At the beginning of the twenty-first century, biologists first deciphered the genomes of many such strains, expecting them to be very similar. False. Two
E. coli
strains can differ in more than one million letters, or one-quarter of their DNA, such that one strain can harbor a thousand genes that the other strain lacks. 22 Every million years—a blip of evolutionary time, 20 percent of the time since humans diverged from chimpanzees—an
E. coli
genome acquires some sixty new genes, all of them through horizontal gene transfer. 23 And these are only the successful edits—many others have gone out of print and left no descendants.
FIGURE 5. Genotype distance
We already know the DNA sequences of more than a thousand bacterial species, and they testify that
E. coli
is not an exception, but the rule. 24 Most bacterial genomes are just as packed with genes trafficked from other sources, many with an unknown origin, though this is scarcely surprising. Trying to discover the provenance of a particular gene is a bit like trying to trace the literary influences revealed in a single paragraph of a novel by reading a small and random selection of the Library of Congress. A thousand species—or even a hundred thousand—would still be a drop in the ocean of bacterial diversity with countless millions of bacterial species, most of them unknown, all of them potential gene donors.
Not all of this genomic change causes metabolic change, because only a third of a genome is devoted to metabolism—the proteins it encodes also have a lot of other business, helping a cell move around, transporting building materials, and so on. 25 So what if gene transfer mostly shuffles the nonmetabolic parts of the genome? Then evolution’s journey through the metabolic library might not take it far, and most metabolisms would therefore be very similar.
Are they? A few years ago, I asked this question of hundreds of bacterial species with known genomic DNA sequences, in a study that relied on decades of research done before my time. This research had discovered thousands of genes that code for particular enzymes, and allowed us to draw maps that connect genes with enzymes, and enzymes with chemical reactions. 26 In other words, we could translate a genome sequence into a metabolic genotype, and compare these genotypes among organisms. 27 And that is what I did.
Figure 5 shows how easy it is to compare two metabolic texts, using the simple example of two short snippets corresponding to ten enzymes in two organisms. Four of the ten enzymes cannot be made by either organism (gray zeroes), six are encoded by the first organism—its genotype string has six ones—and five are encoded by the second organism. We take the number of enzymes (six) made by at least one of the two organisms, and the number of enzymes made by only one but not the other organism (one enzyme), and calculate the
An example of nature’s editorial prowess is our friend
E. coli
and its multiple varieties,
E. coli
strains that were long thought to be like closely related ethnic groups. 21 At the beginning of the twenty-first century, biologists first deciphered the genomes of many such strains, expecting them to be very similar. False. Two
E. coli
strains can differ in more than one million letters, or one-quarter of their DNA, such that one strain can harbor a thousand genes that the other strain lacks. 22 Every million years—a blip of evolutionary time, 20 percent of the time since humans diverged from chimpanzees—an
E. coli
genome acquires some sixty new genes, all of them through horizontal gene transfer. 23 And these are only the successful edits—many others have gone out of print and left no descendants.
FIGURE 5. Genotype distance
We already know the DNA sequences of more than a thousand bacterial species, and they testify that
E. coli
is not an exception, but the rule. 24 Most bacterial genomes are just as packed with genes trafficked from other sources, many with an unknown origin, though this is scarcely surprising. Trying to discover the provenance of a particular gene is a bit like trying to trace the literary influences revealed in a single paragraph of a novel by reading a small and random selection of the Library of Congress. A thousand species—or even a hundred thousand—would still be a drop in the ocean of bacterial diversity with countless millions of bacterial species, most of them unknown, all of them potential gene donors.
Not all of this genomic change causes metabolic change, because only a third of a genome is devoted to metabolism—the proteins it encodes also have a lot of other business, helping a cell move around, transporting building materials, and so on. 25 So what if gene transfer mostly shuffles the nonmetabolic parts of the genome? Then evolution’s journey through the metabolic library might not take it far, and most metabolisms would therefore be very similar.
Are they? A few years ago, I asked this question of hundreds of bacterial species with known genomic DNA sequences, in a study that relied on decades of research done before my time. This research had discovered thousands of genes that code for particular enzymes, and allowed us to draw maps that connect genes with enzymes, and enzymes with chemical reactions. 26 In other words, we could translate a genome sequence into a metabolic genotype, and compare these genotypes among organisms. 27 And that is what I did.
Figure 5 shows how easy it is to compare two metabolic texts, using the simple example of two short snippets corresponding to ten enzymes in two organisms. Four of the ten enzymes cannot be made by either organism (gray zeroes), six are encoded by the first organism—its genotype string has six ones—and five are encoded by the second organism. We take the number of enzymes (six) made by at least one of the two organisms, and the number of enzymes made by only one but not the other organism (one enzyme), and calculate the
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