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Citrate Death Spiral

Michael Behe

Michigan State University biologist Richard Lenski and collaborators have just published a terrific new paper in the journal eLife.1 Anyone who wants to see a crystal-clear example of the inherent, unavoidable, fatal difficulties that the Darwinian mechanism itself poses for unguided evolution should read it closely.

The paper concerns the further evolution of a widely discussed mutant strain of the bacterium E. coli discovered during the course of Lenski’s Long Term Evolution Experiment (LTEE). The LTEE is his more-than-three-decades-long project in which E. coli was allowed to grow continuously in laboratory flasks simply to observe how it would evolve.2 As I’ve written before, almost all of the beneficial mutations that were discovered to have spread through the populations of bacteria in the LTEE were ones that either blunted pre-existing genes (decreasing their previous biochemical activity) or outright broke them.3

An Interesting Exception?

There seemed, however, to be one interesting exception.4 One morning after more than 30,000 generations of bacterial growth, one flask of E. coli (out of 12 separate flasks that Lenski maintained for comparison and replication’s sake) seemed cloudier than the other 11 flasks. That indicated substantially more bacteria than usual had grown in the nutrient broth. After much hard laboratory work, Lenski’s group showed that a region of the prodigious bacterium’s DNA that was close to a gene coding for a citrate transporter (that is, a protein whose job is to bring external, dissolved citrate into the cell; citrate is a common chemical that cells metabolize) had duplicated.5 The duplication mutation placed the control region of a different gene next to that of the citrate transporter.

Here’s why that helped. The citrate-transporter gene’s natural regulator causes the gene to be turned off whenever oxygen is around, as it was under the normal laboratory growth conditions at MSU. The second regulator, however, allows the gene it controls to be turned on in the presence of oxygen. The mutation that placed a copy of the regulator of the second gene next to the citrate gene then allowed the citrate gene to be turned on in the presence of oxygen, too. Since for technical purposes there was a lot of dissolved citrate in the nutrient broth, the mutant E. coli could import and metabolize (“eat”) the citrate, which was unavailable to nonmutants. With all that extra food, the mutant grew like crazy, quickly surpassing nonmutants.

The novel result was widely reported, and the conjecture was floated that perhaps the mutant was on its way to forming a new species.6 As I wrote in Darwin Devolves, however, other, much more ominous, genetic results should have tempered any optimism. For example, the citrate mutant had accumulated many of the same beneficial-but-degradative mutations that had previously spread through the population — the new mutation did not, could not, restore them. And later work showed that several more broken genes had been selected in the mutant, apparently to help it metabolize citrate more efficiently.3

A Sick Puppy

The new paper now reports on 2,500 generations of further evolution of the citrate mutant, in nutrient media that contains either citrate alone or citrate plus glucose (as for earlier generations). As always with the Lenski lab, the research is well and thoroughly done. But the resulting E. coli is one sick puppy. Inside the paper they report that “The spectrum of mutations identified in evolved clones was dominated by structural variation, including insertions, deletions, and mobile element transpositions.” All of those are exceedingly likely to break or degrade genes. Dozens more genes were lost. The citrate mutant tossed genetic information with mindless abandon for short term advantage.

In a particularly telling result, the authors “serendipitously discovered evidence of substantial cell death in cultures of a Cit+ clone sampled from … the LTEE at 50,000 generations.” In other words, those initial random “beneficial” citrate mutations that had been seized on by natural selection tens of thousands of generations earlier had led to a death spiral. The death rate of the ancestor of the LTEE was ~10 percent; after 33,000 generations it was ~30 percent; after 50,000, ~40 percent. For the newer set of experiments, the death rate varied for different strains of cells in different media, but exceeded 50 percent for some cell lines in a citrate-only environment. Indeed, the authors identified a number of mutations — again, almost certainly degradative ones — in genes for fatty acid metabolism that, they write with admirable detachment, “suggest adaptation to scavenging on dead and dying cells.”

The degraded E. coli was eating its dead.

Lessons to Draw

Let me emphasize: the only result from the decades-long, 50,000-plus generation E. coli evolution experiment that even seemed at first blush like it had a bit of potential to yield a novel pathway in the bacterium has resulted instead in spectacular devolution. As Lenski and co-authors wrote in Science in 2019 in their dismissive review of Darwin Devolves(which focused strongly on the clear degradation occurring over the course of the LTEE):7

There are indeed many examples of loss-of-function mutations that are advantageous, but Behe is selective in his examples. He dedicates the better part of chapter 7 to discussing a 65,000-generation Escherichia coli experiment, emphasizing the many mutations that arose that degraded function — an expected mode of adaptation to a simple laboratory environment, by the way — while dismissing improved functions and deriding one new one as a “sideshow”. (Full disclosure: The findings in question were published by co-author Richard Lenski.)

The “one new” function was the citrate mutation. I had called it a “side show” in Darwin Devolves precisely because the E. coli of the LTEE were accumulating degradative mutations much faster than any mutations that might with charity be called constructive:3

Interesting as it is, the ambiguous citrate mutation that started the hoopla is a side show. The overwhelmingly important and almost completely unnoticed lesson is that genes are being degraded left and right, both when they directly benefit the bacteria and when they do so indirectly in support of another mutation. The occasional, particularly noticeable modification-of-function or gain-of-FCT mutation can’t turn back the tide of damaging and loss-of-FCT ones.

The more molecular evolutionary work that rolls in, the more the above conclusion becomes a mere truism.

A Great Strength

In their new paper the Lenski group rightfully points out the great strength of its experimental evolutionary system.1

It is rarely feasible to examine evolution in action as organisms invade, colonize, and adapt to a new niche in nature, especially with independently evolving replicates and control populations. In this study, we investigated how E. coli variants with the new ability to grow aerobically on citrate adapted to a novel, citrate-only resource environment in the laboratory.

Exactly. That means the LTEE gives us our clearest insight into the general effects of Darwin’s mechanism, which continues to operate no matter what other processes may also be occurring (I’m looking at you, Extended Evolutionary Synthesis), no matter whether an organism is in a lab or in the wild, no matter which kind of organism — whether microbe, plant, or animal — is subject to its tender care. So, thanks to the Lenski group, we know that devolution is relentless — it never rests. In good times and bad, if a change in a species could help it adapt more closely to its environment, degradative mutations will arrive most quickly by far to offer their assistance. And, of course, under selective pressure a species has no choice but to accept helpful ones, even if that eventually leads to the species languishing. Thanks in very large part to the fine work done over decades at Michigan State we can now be certain that, like the citrate-eating E. coli, as an explanation for the great features of life Darwin’s theory itself is in a death spiral.

References

  1. Blount, Z., et al. (2020). “Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment.” eLife 9: e55414.
  2. Lenski, R. E. (2017). “Convergence and Divergence in a Long-Term Experiment with Bacteria.” The American Naturalist 190: S57-S68.
  3. Behe, M. J. (2019). Darwin devolves: the new science about DNA that challenges evolution. New York, NY, HarperOne, Ch. 7.
  4. Blount, Z. D., C. Z. Borland and R. E. Lenski (2008). “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli.” Proc. Natl. Acad. Sci. USA 105: 7899-7906.
  5. Blount, Z. D., et al. (2012). “Genomic analysis of a key innovation in an experimental Escherichia coli population.” Nature 489: 513-518.
  6. Pennisi, E. (2013). “The man who bottled evolution.” Science 342: 790-793.
  7. Lents, N. H., S. J. Swamidass and R. E. Lenski (2019). “The end of evolution?” Science 363: 590-590.

Photo: Richard Lenski, by Zachary Blount [CC BY-SA 4.0], from Wikimedia Commons.