Pass the Genes, Please

Gene swapping muddles the history of microbes

Thanks to marriage and birth records, human genealogy is relatively simple. Some people, taking for granted that infidelity hasn’t blemished the family history, can trace their genes back hundreds or thousands of years.

Scientists suspect that the bacterium Thermotoga maritima received a surprisingly large number of its genes from distantly related microbes known as archaea. Each circle represents a protein encoded by a T. maritima gene. The color shows whether the closest known match for the protein is made by another bacterium (light blue), eukaryotes (pink), or archaea (yellow). NCBI

Drawing gene-based family trees for microbes offers more of a challenge, biologists are learning. One difficulty stems from microbial infidelity known as horizontal or lateral gene transfer. As scientists tally up all the genes of more and more microbes, they’re realizing that bacteria and other single-celled creatures regularly pick up genetic material from organisms outside their species, even distant relatives.

Horizontal gene transfer is by no means a newfound phenomenon—the spread of antibiotic-resistance genes drew attention to it decades ago. However, the recent sequencing of microbial genomes reveals that horizontal transfers have occurred far more often than most researchers had appreciated. In a study of the common gut bacterium Escherichia coli, for example, investigators calculate that nearly 20 percent of its DNA originated in other microbes.

The surprisingly large extent of gene swapping has researchers asking whether comparisons of genes indicate how closely related different microbes are and if such analyses can truly point the way back to a universal ancestor. Furthermore, some biologists now argue that gene-transfer events lead to new bacterial species and can help explain why some microbes are harmless while others cause disease.

Even Gary J. Olsen of the University of Illinois at Urbana-Champaign, one of the scientists who vigorously defends using genes to establish microbial lineages, acknowledges that the genes passed between microbial species may be as important as those passed down within a species.

“I see [horizontal gene transfer] as one of the real major forces in evolution,” he says. “It’s totally changed how I think about evolutionary history.”

Horizontal transfer

When it comes to horizontal gene transfer, most of the new research has focused on bacteria. While they don’t have what Dr. Ruth would consider sex, bacteria exchange or take in new genes in several ways.

In a process called conjugation, bacteria physically interact so that DNA moves freely from one cell to another. Plasmids, which are loops of DNA independent of a bacterium’s primary chromosome, move between bacteria during conjugation.

Alternatively, a snippet of DNA wrapped in a piece of cellular membrane may bud off from one bacterium and be absorbed by another cell. Bacteria can also sop up free-floating DNA, released when other cells die and break apart.

Lastly, viruses called bacteriophages, which reproduce within bacteria, can introduce genes that change their host’s capabilities. The viruses inject their genes into a bacterium and force it to make new copies of the virus, which then infect other bacteria. The bacterium that causes cholera, Vibrio cholerae, turns out to be harmless unless it harbors a bacteriophage whose genes encode several toxins (SN: 6/29/96, p. 404). Over time, such phage genes can integrate into a bacterium’s own chromosome.

The first rush of interest in horizontal gene transfer occurred in the 1960s, recounted W. Ford Doolittle of Dalhousie University in Halifax, Nova Scotia, at the American Society for Microbiology meeting in Los Angeles in May. Early on, scientists recognized that antibiotic resistance can spread among bacteria via genes located on plasmids. In the 1970s and 1980s, however, microbiologists became skeptical of the growing number of claims of horizontal gene transfer, notes Doolittle.

During this cautious period, most scientists grew to believe that genes enabling a bacterium to quickly adapt to new environments, such as ones for drug resistance or virulence factors, could be subject to frequent horizontal gene transfer. Yet, they argued, bacteria are unlikely to transfer genes for more fundamental processes, such as cell division.

Only in recent years has that perception changed, notes Doolittle. Now, he says, the crucial question has become whether there are any genes, fundamental or not, that can’t be exchanged.

How do scientists determine that a bacterium’s gene is a transfer? Not easily. “Rigorous proof of horizontal transfer is a difficult matter,” remarks Eugene Koonin of the National Center for Biotechnology Information in Bethesda, Md.

“There’s been a long history of people assuming lateral transfer when they didn’t have the evidence,” adds Olsen.

In one strategy for detecting a swap, scientists identify genes possessed by one bacterial species but not by closely related species. Consider the scenario in which a related group of bacterial species all have a particular gene. If investigators then find that a distantly related bacterium also contains the gene but its closest relatives don’t, they have two explanations to consider.

First, the gene may have existed in the common ancestor of all the bacteria and was simply lost in some species over time. Second, the distantly related bacterium could have recently gotten the gene by horizontal transfer from the first group of bacteria.

Until the past few years, microbiologists were more willing to choose the first option to explain such out-of-place genes. With the flood of recently unveiled microbial genomes, though, they’re seeing more of these cases. At some point, it becomes simpler to assume that a single gene transfer occurred than that all but one of a family of related bacteria lost exactly the same gene, contends Doolittle.

Recent analyses

Some recent genome analyses have hinted at the magnitude of horizontal gene transfer. In early 1998, investigators announced they had deciphered the complete DNA sequence of Aquifex aeolicus, a bacterium known as a hyperthermophile because it can survive temperatures reaching 95ºC. Later that year, Koonin and several colleagues studied the proteins encoded by A. aeolicus genes and looked for similar molecules in a database of previously discovered proteins from other microbes and animals.

To their surprise, they found that the closest matches for about 16 percent of A. aeolicus‘ proteins were in microbes that weren’t even bacteria. They belonged to archaea, microorganisms now considered to be a branch of life separate from bacteria and from eukaryotes, which include plants, animals, and all creatures whose cells have a nucleus.

Koonin and his colleagues took this and other data as evidence that A. aeolicus and archaea had a massive exchange of genes at some point in their history. Since many archaea are also hyperthermophiles and may be the most ancient life-forms on the planet, the investigators speculate that the archaea gave genes to A. aeolicus rather than the other way around. Moreover, suggests Koonin, those genes may have endowed A. aeolicus with its ability to thrive at high temperatures.

Last year, Karen E. Nelson of the Institute for Genomic Research in Rockville, Md., and her colleagues also reported evidence for massive gene transfer between bacteria and archaea. When the scientists sequenced the genome of the hyperthermophilic bacterium Thermotoga maritima, they found that 24 percent of its genes were most similar to known archaea genes.

Olsen and other scientists have challenged such analyses, arguing that they exaggerate the amount of horizontal gene transfer. Among the concerns is that biologists have fully deciphered the genetic sequences of fewer than three dozen microbes, most of them human pathogens. The genes in the databases don’t fairly represent the true diversity of microbial life, the skeptics claim. For example, there may be undiscovered bacteria whose genes more closely match those of T. maritima than archaea genes do.

Sidestepping criticism

In an attempt to sidestep such criticisms, some investigators have sought alternative methods for gauging the extent of horizontal gene transfer. Even without knowing of related genes in other species, biologists can identify swapped genes in a bacterium by their atypical DNA sequences.

Like all DNA, bacterial genes consist of strings of the four nucleotide bases that geneticists abbreviate as A, T, C, or G. Biologists have found that the proportions of these bases differ between species. For example, G and C represent 52 percent of the bases in E. coli DNA but the G-C content of other bacteria ranges from 25 to 75 percent.

Armed with this knowledge, Jeffrey G. Lawrence of the University of Pittsburgh and Howard Ochman of the University of Arizona in Tucson have scanned the E. coli genome for DNA regions where G-C content diverges from the bacterium’s norm. This strategy, which the researchers call molecular archaeology, indicates that 755 of E. coli‘s 4,288 genes were introduced into the bacterium from other microbes in the 100 million years since it diverged from the lineage it shares with Salmonella.

That’s actually a conservative estimate of how much horizontal gene transfer has influenced E. coli, stresses Ochman. Over time, the base content of a foreign gene normalizes to that of its new home, which means that G-C analysis can’t often detect ancient transfer events.

In the May 18 Nature, Ochman, Lawrence, and Eduardo A. Groisman of the Washington University School of Medicine in St. Louis review G-C analyses of several other bacteria and conclude that the microbes “have obtained a significant proportion of their genetic diversity through the acquisition of [DNA] sequences from distantly related organisms.”

They further propose that such acquisitions pave the road for the creation of additional bacterial species by endowing microbes with newfound skills that let them exploit novel niches in their environments. In the case of E. coli, the researchers suggest, the introduction of the lac operon—a cluster of genes encoding proteins that metabolize the milk sugar lactose—probably permitted the bacterium to establish its current home in the colons of mammals. “Horizontal gene transfer drives the diversification of bacterial species,” concludes Ochman.

Evolving new forms

While gene swapping may help bacteria evolve into new forms, it could also prevent scientists from discerning the evolutionary history of those microbes. For decades, the main tools in that quest have been the many genes that encode subunits of ribosomes, the complex protein-making factories within all cells. In particular, the gene for the ribosomal subunit 16S rRNA has served as the foundation for most evolutionary studies.

Since this gene seems to evolve slowly, biologists have compared its DNA sequence in various microbes to determine their relationships and build family trees. Indeed, such analyses reveal the expected three main branches of life: archaea, bacteria, and eukaryotes.

There’s been growing concern about this practice, however, because evolutionary trees built on other genes haven’t always matched the 16S rRNA trees. This inconsistency, combined with the realization that genes hop among species more often than expected, has prompted some scientists to dismiss all gene-based evolutionary trees.

That’s going too far, protest Olsen and some other biologists. “There’s no convincing evidence that ribosomal RNA genes or genes for ribosomal proteins are transferred horizontally. Everything happens in biology, but such events would be exceedingly rare,” says Koonin.

Complexity hypothesis

Why would they be rare? James A. Lake of the University of California, Los Angeles and his colleagues have suggested an answer, a principle they call the complexity hypothesis. Essentially, it states that genes whose products interact with many other molecules are less likely to transfer successfully between microbes than are genes whose products have limited contact with other molecules.

This premise arose from the investigators’ classification of genes as either informational or operational. The former typically encode molecules, such as ribosomal subunits, that play a role in converting the information encoded within DNA into a protein. The products of informational genes often must work in concert with many other proteins to perform their task. A ribosome, for example, consists of dozens of molecules.

In contrast, operational genes encode proteins involved in the upkeep of the cell. Many, such as an enzyme that destroys a misfolded protein, may need to interact with just one other molecule.

After studying a half-dozen microbial genomes, Lake and his colleagues noticed that operational genes horizontally transfer with much greater frequency than informational genes. This, they now believe, is because the odds that a microbe will retain a transferred gene is much greater if its product only has to successfully interact with a single new partner rather than many.

Life’s earliest days

Although the pace of gene transfer today impresses scientists, it may pale compared with the gene swapping that went on in life’s earliest days. Carl Woese of the University of Illinois, who first argued that archaea deserved a separate branch on the evolutionary tree, has proposed that the first forms of life on Earth were simple cells—progenotes, Woese dubs them—that engaged in unusually rampant gene swapping.

“The primitive lateral gene transfer envisioned is very unlike that seen today,” he wrote in a 1998 article. “The high frequency of lateral transfer reflected the simplicity of the progenote’s genetic mechanisms and the lack of barriers to lateral exchange.”

If so, early life may have essentially had a communal genome rather than a fixed one for each cell. Indeed, this gene sharing may have encouraged the rapid evolution of life.

“The fact that innovations could easily spread through the population by lateral transfer gave the progenote community enormous evolutionary potential,” says Woese. How’s that for a lesson on the importance of sharing?