Tag Archives: genetics

On the Evolution of Citrate Use

Those who follow the long-term evolution experiment (LTEE) with E. coli know that the most dramatic change we have observed to date is the origin of the new ability to grow on citrate. It’s dramatic for several reasons including the fact (external to the LTEE) that E. coli has been historically defined as a species based in part on its inability to grow on citrate in oxic environments and the fact (internal to the LTEE) that it was so difficult for the bacteria to evolve this ability that only one of the populations did so, and that it took over 30,000 generations even though an abundance of citrate has been present in the medium throughout the LTEE. Even after 64,000 generations, only the Ara–3 population has evolved that new ability.

Zachary Blount, formerly a graduate student and now a postdoc in my lab, has spent the last decade studying the evolution of this population and its new ability. His two first-authored papers in PNAS (2008) and Nature (2012) demonstrated, respectively, that (i) the origin of the ability to grow on citrate in the LTEE was contingent on one or more “potentiating” mutations that happened before the “actualizing” mutation that conferred the new function first appeared, and (ii) the actualizing mutation was a physical rearrangement of the DNA that brought together a structural gene, citT, that encodes a transporter and a previously unconnected regulatory region to generate a new module that caused the phenotypic transition to Cit+. These papers presented and discussed much more than these two points, of course, but they are the key findings. More recently, Zack was a coauthor on a paper in eLife (2015) by Erik Quandt, Jeff Barrick, and others that identified two mutations in the gene for citrate synthase—one that potentiated the evolution of citrate utilization, and another that subsequently refined that new function.

So we were keenly interested when we saw a new paper titled “Rapid evolution of citrate utilization by Escherichia coli by direct selection requires citT and dctA” by Dustin Van Hofwegen, Carolyn Hovde, and Scott Minnich. The paper is posted online as an accepted manuscript by the Journal of Bacteriology. What follows here are some overall impressions of their paper that Zack and I put together. We may follow these impressions later with some further analysis and comments.

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Let’s begin by saying that it’s great to see other groups working on interesting systems and problems like the evolution of citrate utilization in E. coli.

Moreover, the actual science that was done and reported looks fine and interesting, though we have a few quibbles with some details that we will overlook for now. By and large, the work confirms many of the findings that were reported in our papers cited above:

(i) the ability to grow on citrate in the presence of oxygen can and does evolve in E. coli (Blount et al., 2008);

(ii) when aerobic growth on citrate evolves, it does not do so quickly and easily (Blount et al., 2008) but instead takes weeks or longer—more on that below;

(iii) all strains that have evolved this new ability have physical rearrangements that involve the citT gene and appear also to involve a so-called “promoter capture” whereby a copy of this transporter-encoding gene acquires a new upstream regulatory region (Blount et al., 2012); and

(iv) genetic context matters—the strain one uses affects the likelihood of evolving the Cit+ function (Blount et al., 2008) and the resulting ability to grow on citrate (Blount et al., 2012; Quandt et al., 2015).

The problem, then, is not with the experiments and data. Rather, the problem is that the results are wrapped in interpretations that are, in our view, flawed and fallacious.

“No new genetic information”

The authors assert repeatedly (last sentence of their Importance statement, and first and last paragraphs of their Discussion) that “no new genetic information evolved.” However, that statement flatly contradicts the fact that in their experiments, and ours, E. coli gained the new ability to grow on citrate in the presence of oxygen. We would further add (which we have not emphasized before) that these Cit+ strains can grow on citrate as a sole carbon source—when E. coli grows anaerobically on citrate, it requires a second substrate for growth in order to use the citrate (a phenomenon called “co-metabolism”).

The claim that “no new genetic information evolved” is based on the fact that the bacteria gained this new ability by rearranging existing structural and regulatory genetic elements. But that’s like saying a new book—say, Darwin’s Origin of Species when it first appeared in 1859—contains no new information, because the text has the same old letters and words that are found in other books.

In an evolutionary context, a genome encodes not just proteins and patterns of expression, but information about the environments where an organism’s ancestors have lived and how to survive and reproduce in those environments by having useful proteins, expressing them under appropriate conditions (but not others), and so on. So when natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria.

That’s how evolution works—it’s not as though new genes and functions somehow appear out of thin air. As the bacterial geneticist and Nobel laureate François Jacob wrote (Science, 1977): “[N]atural selection does not work as an engineer works. It works like a tinkerer—a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him, whether it be pieces of string, fragments of wood, or old cardboards; in short, it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.”

To say there’s no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science. In this regard, it seems relevant to point out that the corresponding author, Scott Minnich, is a fellow of the Discovery Institute and was an expert witness for the losing side that wanted to allow the teaching of “intelligent design” as an alternative to evolution in public schools in the landmark Kitzmiller v. Dover case.

“Rapid evolution of citrate utilization”

In the title of their paper and throughout, Van Hofwegen et al. emphasize that, in their experiments, E. coli evolved the ability to grow aerobically on citrate much faster than the 30,000 generations and ~15 years that it took in the LTEE. That’s true, but it also obscures three points. First, we already demonstrated in replay experiments that, in the right genetic background and by plating on minimal-citrate agar, Cit+ mutants sometimes arose in a matter of weeks (Blount et al. 2008). Second, rapid evolution of citrate utilization—or any evolution of that function—was not a goal of the LTEE. So while it is interesting that Van Hofwegen et al. have identified genetic contexts and ecological conditions that accelerate the emergence of citrate utilization (as did Blount et al., 2008), that in no way undermines the slowness and rarity of the evolution of this function in the context of the LTEE (or, for that matter, the rarity of Cit+ E. coli in nature and in the lab prior to our work). Third, the fastest time that Van Hofwegen et al. saw for the Cit+ function to emerge was 19 days (from their Table 1), and in most cases it took a month or two. While that’s a lot faster than 15 years, it’s still much longer than typical “direct selections” used by microbiologists where a readily accessible mutation might confer, for example, resistance to an antibiotic after a day or two.

So while we commend the authors’ patience, we do not think the fact that their experiments produced Cit+ bacteria faster than did the LTEE is particularly important, especially since that was not a goal of the LTEE (and since we also produced them much faster in replay experiments). However, in a manner that again suggests an ulterior nonscientific motive, they try to undermine the LTEE as an exemplar of evolution. The final sentence of their paper reads: “A more accurate, albeit controversial, interpretation of the LTEE is that E. coli’s capacity to evolve is more limited than currently assumed.” Alas, their conclusion makes no logical sense. If under the right circumstances the evolution of citrate utilization is more rapid than it is in the LTEE, then that means that E. coli’s capacity to evolve is more powerful—not more limited—than assumed.

“Speciation Event”

To us, one of the most interesting facets of the evolution of the citrate-using E. coli in the LTEE is its implications for our understanding of the evolutionary processes by which new species arise. Part of the reason for this interest—and the one that’s most easily stated in a popular context—is that the inability to grow on citrate is part of the historical definition for E. coli as a species, going back almost a century. But the deeper interest to us lies not in labeling a new species or debating where to draw the line between species—various criteria are used by different scientists, and inevitably there are many cases that lie in grey areas. Rather, as evolutionary biologists, we are most interested in the process of speciation—the ecological and genetic dynamics that lead to changing biological forms that, over time, are more and more like a new species until, eventually, perhaps far in the future, there is no doubt that a new species has evolved.

In short, speciation is not an event. As Ptacek and Hankison (2009, in Evolution: The First Four Billion Years) put it, “[S]peciation is a series of processes, with a beginning stage of initial divergence, a middle stage wherein species-specific characteristics are refined by various forces of evolution, and an end point at which a new species becomes a completely separate evolutionary lineage on its own trajectory of evolutionary change with the potential for extinction or further diversification into new lineages.” We realize that scientists (ourselves included) often use shorthand and jargon instead of writing more carefully and precisely. We have no doubt that one can find solid scientific papers that talk about speciation events; but except for cases that involve hybridization leading to polyploids that are reproductively isolated in a single generation (as sometimes occurs in plants), this is simply an imprecise shorthand.

In our first paper on the citrate-using E. coli that arose in the LTEE, we clearly emphasized that becoming Cit+ was only a first step on the road to possible speciation (Blount et al., 2008). One criterion that many biologists would apply to investigate speciation is whether a later form merely replaced an earlier form (evolution without speciation) or, alternatively, one lineage split into two lineages that then coexisted (incipient speciation). In fact, we showed that, after the new function evolved, the Cit+ and Cit lineages coexisted (and their coexistence was confirmed using genomic data in Blount et al., 2012). We concluded the 2008 paper by asking explicitly: “Will the Cit+ and Cit– lineages eventually become distinct species?” (emphasis added) and discussing how we might assess their ongoing divergence.

By contrast, Van Hofwegen et al. dismiss the idea of speciation out of hand, not only by calling it an event but by treating the issue as though it hinges, literally, on the individual mutations that produced a Cit+ cell. For example, they write: “[B]ecause this adaptation did not generate any new genetic information … generation of E. coli Cit+ phenotypes in our estimation do not warrant consideration as a speciation event.” And in the penultimate sentence of their paper, they say: “[W]e argue that this is not speciation any more than any other regulatory mutant of E. coli.” (We also note that this is a rather bizarre generalization, as though the gain of function that gave access to a new resource is equal in regards to its speciation potential to, say, the loss of regulation of a function that is no longer used by a lineage in its current environment. Both might well be adaptations, but one seems much more likely to begin the process of speciation.)

In conclusion, Van Hofwegen, Hovde, and Minnich have done some interesting experiments that shed further light on the nature of the mutations and ecological conditions that allow E. coli cells to evolve the ability to grow aerobically on citrate, a function that this species cannot ordinarily perform. However, they misunderstand and/or misrepresent the relevance of this system for evolutionary biology in several important respects. 

And the meaning of historical contingency

The paper by Hofwegen et al. is accompanied by a commentary by John Roth and Sophie Maisnier-Patin. Their abstract begins: “Van Hofwegen et al. demonstrate that E. coli rapidly evolves ability to use citrate when long selective periods are provided. This contrasts with the extreme delay (15 years of daily transfers) seen in the long-term evolution experiments of Lenski and coworkers. Their idea of ‘historical contingency’ may require reinterpretation.”

Historical contingency is a complicated notion, but it essentially means that history matters. In Blount et al. (2008), we made it clear what we mean by historical contingency in the context of the evolution of the Cit+ lineage in one of the LTEE populations. Was this an extremely rare event that could have happened at any time? Or did it instead depend on the occurrence of a sequence of events, a particular history, whereby an altered genetic context evolved—a potentiated background—in which this new function could now evolve?

Roth and Maisnier-Patin’s suggestion that our idea of “historical contingency” may require reinterpretation reflects a false dichotomy between historical contingency, on the one hand, and the effects of different selection schemes, on the other. The fact that evolution might be fast and not contingent on genetic background (though the evidence of Van Hofwegen et al. is, at best, ambiguous in this regard) in one set of circumstances has no bearing on whether it is contingent in another set of circumstances. The historical contingency of Cit+ evolution is not mere conjecture. We showed that the evolution of this new function in the LTEE was contingent. In replay experiments, Blount et al. (2008) showed that that the Cit+ trait arises more often in later-generation genetic backgrounds than in the ancestor or early-generation backgrounds. Moreover, Blount et al. (2012) performed genetic manipulations and showed that a high-copy-number plasmid carrying the evolved module that confers the Cit+ function had very different phenotypic effects when put in a Cit clone from the lineage within which Cit+ evolved than when placed in the ancestor or even other late-generation lineages not on the line of descent leading to the emergence of the Cit+ bacteria. In the clone on the line of descent, this module conferred strong, immediate, and consistent growth on citrate. In the other genetic backgrounds, growth on citrate was weak, delayed, and/or inconsistent.

The hypothesis of historical contingency is not mutually exclusive with respect to causal factors of an ecological or genetic nature—it simply says that factors that changed over time were important for the eventual emergence of Cit+. Moreover, historical contingency was invoked and demonstrated in a specific context, namely that of the emergence of Cit+ in the LTEE—it does not mean that the emergence of Cit+ is historically contingent in other experimental contexts, nor for that matter that other changes in the LTEE are historically contingent—in fact, some other evolved changes in the LTEE have been highly predictable and not (or at least not obviously) contingent on prior mutations in the populations (e.g., Woods et al., PNAS, 2006). [For more on historical contingency and the LTEE, you can download a preprint of Zack’s latest paper from his website: Blount, Z. D. A Case Study in Evolutionary Contingency. Studies in the History and Philosophy of Biology and Biomedical Sciences.]

Erik Quandt offers this analogy to illustrate our point that contingency depends on context: “It’s kind of like the difference between being an average person attempting to dunk a basketball when all by yourself, with unlimited time, and maybe even with a trampoline versus having to get to the rim in a game with LeBron James and the Cavs playing defense. Just because you can do it by yourself under optimal conditions, does this negate the difficulty of doing it in an NBA game or say anything about the kind of history (training and/or genetics) that you would need for that situation?”

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LTEE lines centered on citrate #11

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A Day in the Life of …

Today was a great day – busy and wonderful. Pretty typical, I’m happy to say, though a bit busier than usual but all of it great.

Woke up to beautiful Spring day in East Lansing and walked 1.7 miles to work at MSU.

Did the usual email stuff.

Worked on getting ready for teaching for a class on evolutionary medicine taught by my colleague Jim Smith. Today’s focus will be the paper by Tami Lieberman et al. on the evolution of Burkholderia dolosa in cystic fibrosis patients during an outbreak in Boston. Last night I re-read the paper for the umpteenth time, and I still enjoyed it. Today I organized a series of questions for the students – a very interactive and smart group – around three parts.

Part I: Some background about CF, the inheritance of this disease, the frequency of the disease, how that frequency allows one to estimate the frequency of carriers, why the allele might be so common (not understood), side questions about sickle-cell anemia and why it’s so prevalent, and why, if it’s inherited, the paper we read is all about infections.

Part II: Preparing slides so we could work our way, figure by figure and panel by panel, through all of the main points in Lieberman et al.  (Reminder: Explain to students how scientific papers are often written around figures.  Once the figures and tables are there, then start on the results, etc.)

Part III: Follow up questions about the paper, the system, the interface of epidemiology and evolutionary biology, prospects for the future of this field and the students’ careers (most in this class are premed, many with a research bent), etc. And whatever questions they might want to ask of me.

Sometime in the middle of doing all that: Chatted with second-year grad student Jay Bundy, who is reading some of Mike Travisano’s terrific earlier papers on the LTEE. Specifically, why do we sometimes express fitness as a ratio of growth rates (measured in head-to-head competitions) and sometimes as a difference in growth rates?

Also in the middle of doing all that: Had phone conversation with former Ph.D. student Bob Woods, now also an M.D. specializing in infectious disease, about a faculty job offer he has (congrats, Bob!), some of the issues he needs to clarify or negotiate, and some of the amazing work he’s now doing on the population dynamics and evolution of nasty infections.

Email from grad student Mike Wiser that our paper, submitted to PLOS ONE, has been officially accepted. We had posted a pre-submission version at bioRxiv – now it’s gone through peer-review and revisions and is accepted for publication. Congrats, Mike!

Got a draft of the fourth and final chapter of Caroline Turner’s dissertation. The first three chapters are in great shape. Congrats, Caroline! With teaching looming, I had only time to review the figures, tables, and legends on this one, and made some small suggestions. On to the text tomorrow … It’s a beautiful body of work on two fascinating aspects of the interplay between ecology and evolution that have emerged in the LTEE and another evolution experiment that Caroline performed. Stay tuned for these papers!

Took a phone call from an MSU colleague who has friend with a child in high school who is interested in microbiology, who is visiting MSU, and who wanted to see the lab. Yikes, I gotta run teach! But postdoc Zack Blount kindly agreed to give a guided tour as I headed off to teach.  Thanks, Zack!

Beautiful day continues as I walk to teach in another building. Touch base with Jim Smith about what I plan to cover.

Two straight hours of teaching (one 5-minute break) in an overly hot room. Almost all of it interactive, with me asking questions and the students conferring in small groups and then responding. Very interactive, very bright students! The two hours were nearly up, with little time for my third, post-paper set of questions. But all of the students stayed (despite the beautiful weather, hot room, and the dinner hour at hand) an extra 15-20 minutes for a couple of my questions and some great ones from them about the LTEE and the future prospects for microbial evolution in relation to medicine.

It’s 6:20 pm: I’m mentally exhausted but equally invigorated. Beautiful Spring day continues as I walk home. I’m greeted by our lovely hound, Cleopatra. Exercise and feed her. Then an even more lovely creature, Madeleine, returns home and I greet her.

Check email before dinner. Find that paper with grad student Rohan Maddamsetti and former postdoc Jeff Barrick has been provisionally accepted, pending minor revisions, at Genetics. We posted a pre-submission version of that paper, too, at bioRxiv. Though we still need to do some revisions, I think it’s fair to offer congrats to Rohan and Jeff, too!

Time to crack open a bottle of wine and have some dinner. Fortunately, some of the pre-packaged dinners are pretty tasty and healthy, too, these days ;>)

Refill wine glass. Sit down and start to write a blog on a day in the life of …

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Questions from Jeremy Fox about the LTEE, part 2

EDIT (23 June 2015): PLOS Biology has published a condensed version of this blog-conversation.

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This is part 2, I guess, of my response to Jeremy Fox from his questions about the LTEE over at the Dynamic Ecology blog.

It’s not an answer to his 2nd question, but it’s a partial answer to the first part of his 3rd question? (Have I got you confused already? Me, too.) Well anyhow, Jeremy asked:

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  • Did the LTEE have any hypotheses initially, and if so, how were you going to test them? This question probably just reflects laziness on my part, not having gone back and read the first publications arising from the LTEE, sorry. 🙂 I ask because, with just one treatment and no quantitative a priori model of how the experiment should turn out, it’s not clear to me how it initially could’ve been framed as a hypothesis test. For instance, I don’t see how to frame it as a test of any hypothesis about the interplay of chance and determinism in evolution. It’s hard to imagine getting any result besides some mixture of the two, and there’s no “control” or a priori theoretical expectation to compare that mixture to. Am I being dense here? (in addition to being lazy…)

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Short answer: Yes, the LTEE had many hypotheses, some pretty clear and explicit, some less so. (What, did you think I was swimming completely naked?)

Medium answer that will be fleshed out in later responses: Before we get to specific hypotheses—those formal, testable suppositions and predictions—I like to begin with general questions about how and why things are they way they are. So, what were the questions the LTEE originally set out to answer? (I emphasize “originally” because new or substantially refined questions have arisen over the course of the project, as we’ve answered some questions, made new observations, framed new questions, etc.)

What follows below are three overarching sets of questions that I hoped, long ago, the LTEE could answer, at least in the context of the simple flask-world that it encompassed. I present all three sets of questions  in some of my talks about the LTEE. However, in my talks to broad public audiences – like my Darwin Day talk at the University of Calgary next week – I focus especially on the third set of questions – about the repeatability of evolution – because I think it is the most interesting to people who are not necessarily evolutionary biologists or even scientists, but who are curious about the world in which we live.

Motivating questions for the LTEE

A few more thoughts: The first set of questions, about the dynamics of adaptation, include ones where I had clear  expectations that were testable in a fairly standard hypothesis-driven framework. For example, I was pretty sure we would see the rate of fitness improvement decelerate over time (and it has), and I was also pretty sure we’d see a quasi-step-like dynamic to the early fitness increases (and we did). Nonetheless, these analyses have yielded surprises as well, including evidence (and my new strong conviction) that fitness can increase indefinitely, and essentially without limit, even in a constant environment. In regards to the second set of questions, about the dynamics of genome evolution and their coupling to phenotypic changes–I’m sure these were part of my original thinking, but I will readily admit that I had almost no idea how I would answer them. Hope sprung eternal, I guess; fortunately, wonderful collaborators—like the molecular microbiologist Dom Schneider—and brand new technologies—wow, sequencing entire genomes—saved the LTEE.

 

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Putting GMOs on a Tight Leash

Two papers appeared in the latest issue of Natureone from Farren Isaacs’ group and the other from George Church and colleagues—that presented, developed, and demonstrated a strategy for limiting the spread of genetically modified organisms, or GMOs, in the event that they are accidentally released or deliberately applied to the environment.

My Involvement with GMO Discussions in the 1980s

I was actively involved in discussions about environmental applications and field testing of genetically engineered organisms back in the 1980s. As a postdoc in 1984, I had a short letter in Nature where I suggested a containment strategy for an early proposed application of genetically modified “ice-minus” bacteria. Later that year I attended a small meeting on environmental applications of GMOs at the Cold Spring Harbor Laboratory, and a short report was published in the Bulletin of the Ecological Society of America. As faculty member at UC Irvine in 1986, I served as a consultant on a report for the Office of Technology Assessment of the US Congress. I also co-organized and moderated a lively public debate on the benefits and risks of genetically engineered organisms between Jerry Caulder, who was CEO of a biotech company, and the distinguished ecologist Daniel Simberloff, an expert on invasive species.

At that time, one of the arguments—the “excess baggage hypothesis”—for the safety of GMOs was that genetically engineered functions would impose a metabolic burden and thereby reduce the fitness of the organisms, so that they wouldn’t be good competitors in nature. While that argument made some sense as a trend or tendency, it didn’t seem likely that it would apply in every possible case given the potential for new environments and/or compensatory adaptations to favor novel functions. In 1988, I wrote a review for Trends in Ecology & Evolution with a postdoc, Toai Nguyen, on the “Stability of recombinant DNA and its effects on fitness” that made these points.

As a result of my interest in and involvement with these issues, I was asked to serve on two expert panels—one convened by the Ecological Society of America (ESA), the other by the National Research Council (NRC) arm of the National Academy of Sciences—that wrote lengthy reports, both published in 1989. In both reports, the committees tried to emphasize that one needed to consider two different issues. (1) What, if any, were the potential problems that might be caused by the release of particular GMO? (2) In the event that some problem actually did arise, would the GMO (or its engineered genes) survive and possibly spread in the environment? Or would the problem be resolved by halting further applications of the GMO, because they would then simply die off?

(These panels were hard work, but through them I met some great scientists, including Jim Tiedje and Rita Colwell among many others.)

After that extensive involvement with this science-policy issue in the 1980s, my research tended toward more basic questions in the years that followed. Meanwhile, of course, there has remained substantial scientific, commercial, and public interest in the methods and applications of genetic engineering. The two recent papers in Nature reflect the latest efforts to ensure the safety of GMOs by putting them on a tight leash.

My Thoughts on the Recent Papers

I was asked to comment on the Nature papers by Malcolm Ritter, a science reporter for the AP, and he briefly (and accurately) quoted me in a short news piece that appeared yesterday. In light of a question about my thoughts on Twitter, I thought I’d share my full remarks here:

Using genetically modified organisms in the environment raises a couple of intersecting issues. One concerns the effects those organisms have. Of course, GMOs are intended to provide some benefit—say, for bioenergy or agriculture—but in some cases the GMOs might have secondary or unanticipated harmful effects. If these harmful effects occur, and if they outweigh the benefits, then one would like to be able to recall the GMOs from the environment—sort of like recalling cars when some problem is discovered after they’ve been sold. The challenge is that GMOs are organisms, they are alive and can reproduce, and so they won’t necessarily just go away if one stops using them. Over the years, different strategies have been proposed to ensure that GMOs will, in fact, just die off after they’ve done their job, but these strategies have had holes, such as the possibility that evolution might break whatever leash the scientists put on the GMOs so that they could be recalled.

These two papers, though, point the way towards putting GMOs on a very tight leash, one that is meant to be unbreakable, by changing the genetic code of an organism so that its replication becomes dependent on certain synthetic building blocks—amino acids—that aren’t found in nature. So by applying these molecules along with the GMO in some environment, the GMOs can replicate and do their job. But if the synthetic amino acids aren’t supplied, then the GMOs won’t be able to replicate further after they’ve run out, and so that provides a leash that should rein the GMOs in if there is some problem. Of course, there are a lot of technical challenges to pulling this off, because you can’t make the organisms so weak that they can’t do their intended functions.

And of course, extending this approach from microorganisms—the subject of these papers—to crop plants would raise all sorts of additional questions about nutritional value and safety. Those are different issues and not what these papers are about.

Coda: Does this approach ensure containment of a GMO? Probably not. There aren’t many guarantees in life, and evolution has a history (billions of years, in fact) of finding clever solutions that might not occur to engineers and scientists. Does that mean that we should not use GMOs in nature? Not at all. As our ESA and NRC reports of a quarter-century ago stressed, one should consider both the benefits of a particular environmental application of a GMO and its potential harm if something goes wrong. In those cases where the benefits are great, and the potential for harm is very small (both in likelihood and magnitude), then the issues of containment and recall after a release are less critical. But in those instances where the potential risks of some GMO are substantial—either in terms of the likelihood or the magnitude of adverse effects—then every effort must be made to put the GMOs on a tight leash or, absent that, do not proceed with the proposed application.

[The image below is one part of Figure 1 from the Nature paper, titled “Recoded organisms engineered to depend on synthetic amino acids” and authored by Alexis J. Rovner, Adrian D. Haimovich, Spencer R. Katz, Zhe Li, Michael W. Grome, Brandon M. Gassaway, Miriam Amiram, Jaymin R. Patel, Ryan R. Gallagher, Jesse Rinehart and Farren J. Isaacs.  This image is shown here under the doctrine of fair use.]

Portion Fig 1 from Rovner et al, Nature, 2015

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An Absence of Posts, an Abundance of Talks, and More

Dear Reader:  No, I have not given up on this blog.  But I’ve been busy, busy, busy!

In the last four weeks alone, I have traveled to the University of Arizona, Harvard University, Duquesne University, and Princeton University.  Besides giving talks at each place (two public lectures and two academic seminars, with cumulative audiences of well over a thousand people), I have met with dozens and dozens of amazing scientists, from graduate students and postdocs to faculty both young and old.  It’s been a blast:  an exhausting blast, but a blast all the same!

And next week?  I’m hosting four terrific colleagues from two continents who will work with me to begin making sense of hundreds of newly sequenced genomes from the LTEE.

Oh, and we have some more job searches starting next week.

And did I mention?  We just had a fascinating (if I may so myself) and complex paper come out today in Science (on-line express for now) on the most deeply divergent (i.e., oldest sustained polymorphism) of the 12 LTEE populations.  And no, it’s not about the citrate eaters from population Ara–3.

Plucain, J., T. Hindré, M. Le Gac, O. Tenaillon, S. Cruveiller, C. Médigue, N. Leiby, W. R. Harcombe, C. J. Marx, R. E. Lenski, D. Schneider.  2014.  Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.  Science.

It’s population Ara–2 instead, where two lineages—dubbed the Larges (L) and Smalls (S)—have coexisted for several tens of thousands of generations.  In superb research led by Dr. Jessica Plucain that she did in the lab of my long-time collaborator (and dear friend!) Prof. Dom Schneider (Grenoble, France), Jessica led the work to identify—out of hundreds of mutations—three that are sufficient to allow a “constructed” S ecotype (i.e., the ancestor plus three derived alleles) to invade and stably coexist with the evolved L ecotype.  Ecological context and specific genetic interactions are key to establishing this “half” of the polymorphism … and the other “half” of the story— what makes the L ecotype special—might well turn out to be just as complex, or perhaps even more so.

The S and L types are especially challenging (even painful!) to work with because this population became a mutator very early on—before the two lineages diverged—and so there are many, many mutations to contend with; moreover, they make colonies on agar plates that are quite challenging to score and count.  So congratulations to Jessica, Dom, and other members of Dom’s lab for their perseverance in studying this extremely interesting population.

Also on the list of authors are Prof. Chris Marx and two members of his lab.  They performed metabolic analyses showing how the carbon fluxes through the central metabolism of the S ecotype have diverged from both the ancestor and the L ecotype.  Chris was a postdoc in my lab almost a decade ago, but most of his work (then and since) has been on experimental evolution using Methylobacterium, and so this is the first paper we’ve co-authored.

There was a production error, though, in the on-line version of our paper; the final sentence of the abstract was dropped (except for one word).  The abstract, in total, should read as follows:

“Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed this lineage to invade and stably coexist with the other. These mutations all affected regulatory genes and collectively caused substantial metabolic changes. Moreover, the particular derived alleles were critical for the initial divergence and invasion, indicating that the establishment of this polymorphism depended on specific epistatic interactions.”

[Edited on 07-Mar-2014:  The on-line PDF at Science Express now has the complete abstract.]

~~~

The picture below shows Dom Schneider and Richard Lenski in Paris in 2013.  They are holding a petri dish that Jessica Plucain made to celebrate the 25th birthday of the LTEE.

Dom and Rich, Paris, 2013

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Zachary Blount on “Ham on Nye” Debate, Follow-up #3

I’m very pleased to present this guest post written by Dr. Zachary Blount, aka Dr. Citrate, as an in-depth follow-up to the “Ham on Nye” science versus creation debate.  Zack did his undergraduate studies at Georgia Tech, and then obtained a masters degree from the University of Cincinnati.  After that, he came to MSU, where he completed his Ph.D. in 2011.  With his doctoral work generating so many interesting results and new questions, Zack stayed on here as a postdoctoral researcher.  His current research is funded by a grant from the John Templeton Foundation Program on Foundational Questions in Evolutionary Biology.

Zack has devoted years to studying the evolution of the ability to grow on citrate that occurred in one of the 12 populations from the long-term evolution experiment (LTEE) with E. coli.  We still don’t fully understand all of the steps involved.  But a simple “on/off” switch it is not!

However, even if it had been a single, simple mutation that allowed the cells to grow on citrate, that still would have been evolution … it still would have been a beneficial mutation in the context of the experiment … and it would still have demonstrated the acquisition of new information encoded in the genomes of the bacteria that fits them to their environment.  Of course, if it were so easy as a single, simple mutation, then we would have seen that capability evolve in many or all of the populations. But after almost 60,000 generations to date, only one population has evolved that ability.

You can read about the technical details of our findings in two papers here and here, as well as in a recent paper from a team at the University of Texas, Austin.

In what follows, the nomenclature Cit+ refers to the bacteria that evolved the ability to grow on citrate in the presence of oxygen, while Cit refers to the bacteria – their ancestors and other E. coli – that lack that ability.

 — Richard Lenski

* * * * *

My work on the evolution of aerobic growth on citrate in one of the LTEE populations has received a fair amount of attention over the years.  (Sometimes there is a bit of a dream-like quality to it all.  I still have a hard time conceiving that people unknown to me know about what this here kid from north Georgia has done.)  The attention is rather gratifying because I’ve spent many years and a great deal of effort in school and in the lab to become an evolutionary biologist. But why did I do all that in the first place? Because I find evolution to be endlessly fascinating, beautiful, and even inspiring.

It means a lot to know that the work I spent several thousands of hours toiling away on has made a contribution to science.  Even more satisfying is that my work has come to be viewed as a go-to example of evolution in action that may, perhaps, inspire in others some of the same feelings that have motived me.

Of course, this attention has also been a bit troubling because it has led to repeated disparagement, dismissal, distortion, and misrepresentation of my work by both professional and amateur creationists.  These creationists often get entirely wrong the work my colleagues and I toiled long and hard to do, likely because they haven’t bothered to read our papers, learn the details and methods, or think much about the results.  (I suspect some duplicity is in there, too.)  Reflexive, unthinking dismissal bothers me – maybe because my parents and devoutly Southern Baptist Granny told me when I was a child that this is something that civilized folk simply should not do.

This brings me to the recent debate between the legendary science educator Bill Nye and the legendary obfuscator and anti-science showman Ken Ham.  It was the standard sort of set-up, with Nye defending evolution and science against creationism, and Ken Ham, well, doing what Ken Ham does.

Twice during the debate, Ham discussed my work with the LTEE population that evolved the capacity to grow aerobically on citrate.  The first time was at about 44 minutes, and included a video clip of Dr. Andrew Fabich, a “Biblical creationist” microbiologist at Liberty University.  [You can read the transcript here.]

The evolution of the new Cit+ function is, and has been discussed as, an instance of evolutionary innovation that arose in a controlled experiment in which we can drill down and figure out how it evolved. Ham and Fabich, however, dismissed Cit+ as an innovation or even an instance of evolution using two arguments suggesting that neither knows the work well at all and likely have not read our papers.  (In Ham’s case, this wouldn’t be surprising, as he has been called “willfully ignorant” even by other creationists, which is a bit like being called unkempt by Pig-Pen or in need of a haircut by Cousin Itt.  In Fabich’s case, however, it would betray a lack of professional courtesy, at best.)

First, Ham repeatedly said that some of the bacteria in the LTEE “seemed” to have developed the ability to grow on citrate.  This wording suggests either stupidity or duplicity on our part, as though we either didn’t check or just lied, but the fact of the matter is that there is no “seem” about it.  The Cit+ bacteria do grow on citrate, and they do so under conditions that E. coli normally does not.  This ability is something that is easy to demonstrate, and which I and my colleagues – not only in the Lenski lab but also other labs that are now working with these bacteria – have documented.  And it’s not as though we don’t have the evidence – as Rich has pointed out to another anti-evolution critic, we have many, many, many vials full of them in our freezers.

The second argument was more direct.  Both Ham and Fabich asserted that the Cit+ function did not evolve because using citrate did not involve “any kind of new information … it’s just a switch that gets turned on and off.”  (Fabich went on to state that this “switch” is what we reported.  That is emphatically not true.  It beggars belief that anyone, much less a trained microbiologist, could actually read our 2012 paper, where we reported the genetic basis of Cit+, and come away thinking this.) Variations on that wording are often used by creationists who discuss the citrate work because it implies that Cit+ arose because of a pre-existing regulatory switch and involved no evolution at all.  But that simply is not the case – that wording, dare I say it, is a lie.

If you take E. coli from a medium in which it is growing on glucose, and move it into a medium where the only thing to eat is something else, like lactose, it turns off the expression of some genes specific to growth on glucose, and it turns on other genes necessary to grow on lactose.  That is what is called gene regulation, and that is what biologists mean when they talk about switching functions on and off – existing genetic circuitry that allows an organism to respond to changes in the external and internal environment.  If you transfer normal, Cit E. coli from a glucose medium to a medium with only citrate to eat, they don’t grow.  They just sit there and starve.  Regular E. coli cells have no existing genetic regulatory circuitry that “flips a switch” to allow them to start growing on citrate in the presence of oxygen.  On the other hand, if you do the same thing with the Cit+ cells that evolved in the long-term experiment, the Cit+ cells will start growing happily on citrate.  This difference is not a matter of gene regulation, but an evolved difference between the ancestral strain and the Cit+ lineage that allows Cit+ cells to grow on citrate.

No, the ability to grow on citrate is not a matter of simply flipping a pre-existing regulatory switch.  Continuing the electrical metaphor, the evolved Cit+ function is instead about rewiring.  My dear little Cit+ cells gained their ability to partake of the previously forbidden citrate by a genetic duplication involving a gene, called citT, which encodes a transporter protein that is used during anaerobic growth on citrate.

This duplication did something very special.  You see, one of the major aspects of gene regulation is that genes have associated regulatory DNA sequences, including what are called promoters that control when genes are expressed.  The citT gene is normally controlled by a promoter that tells the cell to turn it on only when there is no oxygen present.  As shown in the Figure below, the gene duplication put one copy of citT next to, and under the control of, a promoter that normally controls another gene called rnk.  The rnk gene is normally turned on when oxygen is present.  The new association between citT and the rnk promoter – what we call the rnk-citT regulatory module – turns citT on when oxygen is present, and allows Cit+ cells to use citrate under the conditions of the LTEE.  (To really feast on the citrate involved additional evolutionary changes, both before and after this rewiring, but I’ll leave that point aside for this post.)

There is a very interesting consequence of how the rnk-citT module originated. While Ham did not make this argument, other creationists have asserted that Cit+ arose simply by a loss of gene regulation, because they have the notion that evolution can only break things.  However, the duplication that gave rise to the rnk-citT module caused no such thing.  There is still a copy of citT that is linked to the same adjacent DNA sequence as before, and there is still a copy of rnk that is under the control of its own promoter.  In other words, the cell got something new without losing anything old.

When they actually bother to explain all of that, creationists still dismiss Cit+ as being an instance of evolutionary innovation because it involved the rearrangement of existing components.  True, the duplication responsible for Cit+ did rearrange components that were already there, but that rearrangement generated a new association between components that did not previously exist, and it produced a new function that also did not previously exist.  To argue that rearrangements cannot produce innovation is akin to arguing that a novelist has done nothing creative in writing her novels because she only used words that already existed.

Ham also made a demand that is common among creationists that betrays a fundamental misunderstanding of evolutionary theory. In the later debate segment [starting at ~2:30], Ham says, “What Bill Nye needs to do for me is to show me example of something…uh, some new function that arose that was not previously possible from the genetic information that was there. And I would claim and challenge you that there is no such example that you can give… you’d have to show an example of brand new function that never previously was possible.  There is no such example, uh, that you can give anywhere in the world.”

According to Ham, evolution cannot be true if this burden can’t be met.  Consider that wording for a moment, though: “… show an example that never previously was possible.”  Not possible?  That’s kind of a high bar given that impossible things don’t happen by definition.  Moreover, it is clear from Ham’s words that he won’t regard any capacity that arises from modification of an existing genome to be an innovation, which means that he must think that evolutionary theory holds that new genes just pop into existence fully formed, without precursor states, like Athena from the head of Zeus.

This goes to the larger problem with how Ham, Ray Comfort, Michael Behe, Georgia Purdom, and others of their ilk approach evolution – they just don’t know much about it, and so what they end up arguing against isn’t the science, but a caricature of the science that exists only in their minds.  Evolutionary novelty does not arise from genes just popping into existence.  That is a silly idea, and one that no evolutionary biologist holds!

Instead, evolution innovates and creates through descent with modification of what already exists, a process that Nobel laureate François Jacob called “evolutionary tinkering”.  This modification arises by random mutations: base changes, deletions, duplications, insertions, and so on – and, depending on the organisms, horizontal genetic exchange and sexual recombination.  Natural selection then preserves and accumulates the useful changes – those that enhance survival and reproduction of the organism in its environment – across the generations.  Often, such innovations are based on just what we see with the Cit+ bacteria – novel rearrangements of old components.  Indeed, Jacob wrote that, “(Evolutionary) novelties come from previously unseen association of old material.  To create is to recombine.”

So Ham and other creationists dismiss how evolutionary theory says evolution works as not being evolution, and then they demand the impossible.  That strikes me as neither fair nor honest.  But in the end, their lies, distortions, misrepresentations, and ignorance don’t matter, just as debates, entertaining though they may be, don’t matter, because nature doesn’t care.  To paraphrase a bumper sticker I once saw, they may not believe in evolution, but nature does!

While they go on cycling through their old and ossified rhetoric according to their fixed and incorrect notions, evolution proceeds, MacGyvering the new from the old. Natural selection can’t do the impossible, but it is pretty darn spiffy at doing the improbable with the rare.

If you are interested in learning more, please visit my website, where you will find my papers available for download.  You can also watch my Ph.D. defense presentation, in which I go into much more detail about the evolution of the Cit+ E. coli.

— Zachary Blount

* * * * *

The figure below shows schematically the tandem duplication in the population that evolved the new ability to grow on citrate.  This duplication produced the new rnk-citT regulatory module by placing the second copy of the citT gene adjacent to the rnk promoter region.  The figure comes from Blount et al., 2012, Nature; it is shown here under the doctrine of fair use.

tandem duplication

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What We’ve Learned about Evolution from the LTEE: Number 5

This is the fifth in a series of ~10 posts in which I summarize what I think are the most important findings and interesting discoveries from the LTEE.  The previous entry, number 4, also has links to the earlier entries.

Number 5.  We have seen large changes in the spontaneous mutation rate in some of the LTEE populations.  These changes reflect an interesting tradeoff between short-term fitness and long-term evolvability.

Proximate causes.  Six of the 12 LTEE populations evolved to be so-called “hypermutators” by 50,000 generations.  The proximate (i.e., biochemical) causes of these changes are mutations in genes whose products are involved in DNA repair or the degradation of molecules that cause damage to DNA.

These mutations typically cause the rate of point mutations throughout the genome to increase by roughly 100-fold (Sniegowski et al., 1997, Wielgoss et al., 2013), so their effects are not at all subtle.  They also change the spectrum of mutations:  mutations in the mutS gene, which encodes a protein involved in mismatch repair, cause increased A·T–>G·C and G·C–>A·T transitions (Lenski et al., 2003); while mutations in mutT, which encodes an enzyme that degrades an oxidized nucleotide, cause A·T–>C·G transversions (Barrick et al., 2009).

Evolutionary effects.  The evolutionary effects of these hypermutators are subtle and interesting.  In essence, one can think of mutations that produce hypermutators as affecting the tradeoff between short-term fitness and long-term evolvability.

Short-term cost.  Of all the possible mutations that might occur, many more are deleterious than are beneficial. Therefore, hypermutators produce more maladapted progeny than otherwise identical cells with a lower mutation rate.  Hence, hypermutators suffer a fitness cost caused by the increased production of progeny with deleterious mutations.

However, the E. coli strain that was the ancestor to the LTEE has a low point mutation rate, which we’ve estimated as ~10-10 per base-pair per generation (Wielgoss et al., 2011).  Given the genome contains ~5 x 106 base-pairs, this rate translates to only ~0.0005 point mutations per genome per generation.  Therefore, even a 100-fold increase means that most hypermutator progeny are mutation-free.  Considering that only a fraction of genomic sites are subject to mutations that would be deleterious in the LTEE environment, we infer that the short-term cost to a 100-fold hypermutator is ~1% (Wielgoss et al., 2013).

Evolvability benefit.  Even a 1% cost is not trivial, so how can a hypermutator survive and spread through a population?  In fact, most hypermutators do not survive; the vast majority of mutations that cause hypermutators will die out as a consequence of that short-term cost.  However, hypermutators result from loss-of-function mutations, and a dozen or so large genes are targets for these mutations.  Hence, new hypermutators will continually be regenerated in large populations.  Absent other forces, an equilibrium frequency of hypermutators would be reached that reflects the balance between the rate of appearance of hypermutators by new mutations in the relevant genes and the rate at which they are removed by selection against the deleterious mutations they cause—in other words, the familiar mutation-selection balance of population-genetics theory.

But another force is at play: the populations in the LTEE are not sitting on a fitness peak, so there are on-going opportunities for beneficial mutations to appear.  And a hypermutator cell has a much higher probability of generating a beneficial mutation than does a “normal” cell.  In essence, there’s a race to produce the next winner.  If a hypermutable cell generates the next beneficial mutation that sweeps through the population, then the hypermutator will “hitchhike” along with it because, without sex, the two mutations are linked.

Combining forces.  So how do the short-term cost and the evolvability benefit play out together?  Mutations that knock out any one of the genes involved in DNA repair probably occur at a rate between 10-5 and 10-6 per generation, and the resulting hypermutable cells have a fitness disadvantage of ~1% owing to the production of deleterious mutations.  At mutation-selection balance, the frequency of hypermutators is between 0.01% (10-4) and 0.1% (10-3).  Let’s use 0.05% to illustrate.

Although the hypermutators are a small minority, on a per capita basis each of them has a 100-times higher probability than a normal cell of generating the next winner.  So 5% of the time, a hypermutator will be swept to fixation, but most of the time the winner will be produced by a normal cell.  Now consider the fact that each of the LTEE populations has had many beneficial mutations go to fixation over its history.  After 14 selective sweeps, the odds are better than 50:50 that at least one of those beneficial mutations was generated by a hypermutator.

King of the mountain.  After a hypermutator becomes common, it becomes very hard to dislodge it from the population.  This difficulty follows from the same logic as above.  Once the hypermutator reaches 1% of the population, it has a 50% chance of generating the next winner; by the time it gets to a 50% frequency, the odds are 100:1 in its favor.  Thus, a hypermutator only needs to get lucky once, and then it becomes extremely difficult to displace it … at least so long as the population is far from the fitness peak.

Nothing lasts forever.  Even before a population reaches a fitness peak, its rate of fitness improvement typically decelerates, at least in a constant environment like that of the LTEE (Wiser et al., 2013).  At some point, the magnitude of the benefit that would result from reducing the mutation rate and its associated fitness cost may become commensurate with the fitness advantages that are available from other mutations.  When that happens, selection to reduce the mutation rate becomes effective, and the hypermutable “king of the mountain” can be displaced by a genotype with a lower mutation rate.

Indeed, we have observed this displacement occurring in one of the LTEE populations (Wielgoss et al., 2013).  In that population, not one but two lineages independently arose (see Figure below) that reduced the mutation rate by about half, while reducing the fitness cost from ~1% to ~0.5%.  The population thus remains hypermutable, but less so than before.

What the future may hold.  In that paper, we hinted that it is probably easier to reduce the mutation rate in stages rather than to revert to the ancestral rate in a single step.  That’s because the population is continuing to adapt, albeit at a slower rate.  A genotype with a 50% reduction in the mutation rate will save half of the fitness cost of the full-blown hypermutator, yet it will continue to produce 50 times as many other beneficial mutations as would a genotype that reverted to the ancestral mutation rate.  In essence, the fitness costs and the evolvability benefits are on very different scales.

The figure below shows the decelerating fitness trajectory (dark green curve, left axis) and the number of mutations (right axis) as the lineage with the ancestral mutation rate (blue) is replaced by a hypermutator lineage (red), which in turn is displaced by two independent lineages with somewhat lower mutation rates (light green and purple).  The figure comes from Wielgoss et al., 2013, Proc. Natl. Acad. Sci. USA; it is shown here under the doctrine of fair use.

Mutation trajectory, PNAS 2013

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