Antimicrobial resistance represents one of the major global threats to health and development. Mutations are the driving force of evolution, but their phenotype is defined by the existing molecular mechanisms inside cells. By focusing not only on the mutations that lead to adaptation, but also on those that do not, mechanisms that constrain evolution can be uncovered.
We spoke with Dr. Mato Lagator, Wellcome Trust, Royal Society Sir Henry Dale Fellow and presenter of our upcoming webinar, whose team is using synthetic biology to experimentally influence evolution to manipulate bacterial gene regulatory networks. He and his team hope to learn more about the relationship between molecular mechanisms and evolution in the emergence of antimicrobial resistance.
Q: Can you walk us through your background and your path towards the research you are doing?
ML: I was raised as an evolutionary biologist and really got into evolution of microbes largely because I was impatient with my prior work, which was focused on the molecular evolution of birds. I quite like the pacing of microbes because of their rapid growth – you can get really excited about the field of experimental evolution where you can watch and observe how things evolve in real-time. I can put something that is genetically the same strain in different environments today, watch them evolve differently, and actively try to learn something about evolution.
I still think primarily in terms of questions that regard evolution. I found that as I was getting deeper into the field, there’s a lot of work on how different environments shaped evolution but less on how different starting genetic points shape evolution. This got me interested in how we can use synthetic biology to really understand evolution. In other words, using synthetic biology to engineer different starting points genetically and then seeing how those starting genetic points shape the way in which an organism can evolve over time.
The big philosophical vision for my group’s research came about during my postdoc, looking at existing mechanisms in the cell and how something works shapes the way it can change. That seems obvious, but it’s not how most people study evolution. In fact, very few people look at evolution that way. There’s good biophysical understanding of the basic component of regulation – two molecules binding to each other, binding to a protein, binding to DNA – and so we use biophysics to try to understand those mechanisms and how they limit the way in which organisms can change. It allows us to predict the effects of mutations without having to do every experiment in the lab. This is linked to antibiotic resistance and how we can manage that.
Q: Can you share a favorite moment as a scientist when you had one of those breakthrough results?
ML: That’s a cool question. I wouldn’t say there was a ‘eureka moment,’ but there were several periods of time when things suddenly came together. I think a few big breakthroughs happened during my postdoc work. I was just doing things that seemed interesting, but there wasn’t a sense of vision for how they came together. What seemed like very separate projects to me – even though they were linked as I was working on E. coli regulation studies – suddenly came together conceptually under the auspice of uncovering mechanisms, how things work, and what that means for how they can change. That was the philosophical and transitional point, where I thought, “Okay, this feels like something I can now do as a group leader”. It felt like a vision of how we’re doing something differently in our research that was original and exciting.
Q: What is driving the rapid rise of antibiotic resistance? Is it simply overuse of antibiotics?
ML: To be honest, I don’t really know. It’s an evolutionary problem and the reason why I started thinking about this is because I was at a couple of different conferences that showcased new approaches to tackling resistance. I was one of the very few evolutionary biologists there, which was interesting because it’s such a fundamental evolutionary phenomenon. It’s rare that evolutionary biology, in its 150-year history, has had a moment where it’s actually studying something that is genuinely impactful for human life. So, it’s hard to answer that question as to where it comes from. Sure, I can answer it on a very broad level; we use antibiotics and resistance will happen. That’s literally true, right? Bacteria will figure it out.
We also use antibiotics questionably a lot of the time. A colleague of mine, Chris Knight, once stated that the way we use antibiotics in clinics, and particularly in agriculture, is as if we want bacteria to become resistant as fast as possible and I have to agree. I think it’s a challenge, particularly for evolutionary biologists. How can we use them differently? And what can we do better in addition to exploring new approaches like phage therapy, for example?
A while back, I was talking to a clinician who told me that Manchester, UK especially North Manchester, has a large problem with antibiotic-resistant gonorrhea. They were looking at the history of the use of antibiotics in individual patients. After examining individual patient records, there were patients who, for 7, 8, or 9 times in a two or three-year period, would come back to the general practitioner and get prescribed the same antibiotic for the same infection. This shows how generally there is a large focus on the development of new drugs including new antibiotics and improving effectiveness, but not on long-term sustainability.
Q: Why is it important to study the evolutionary processes underlying the emergence of resistance versus exploring new ways to combat resistance?
I don’t think one is more important than the other so I wouldn’t say “versus.” What I would say is that there is an incomplete understanding of the evolutionary aspects of this problem. It’s hard for me to conceptualize how we deal with this challenge, especially in a long-term sense, without understanding the nature of the problem. I mean, that’s sort of what got us into this mess, right? We had antibiotics that worked, it’s all fantastic, and then not so much anymore.
Even when we think about phage therapy, that’s also an evolutionary situation in which you must understand how those bacteria are going to respond. There’s often this hope or dream of how we’re going to find an evolution-proof approach, which is unrealistic. As an example, if you put E. coli with any “evolution-proof solution” for four days, you will realize you just can’t kill them. You need to find ways for long-term effectiveness.
Q: How does next generation sequencing (NGS) technology support your research?
One of the big things that we’re interested in is understanding the biophysical parameters that determine how a given transcription factor binds DNA. Each transcription factor, just like any protein, can be thought of as an amino acid sequence —but that’s just a representation of the protein and not really what the protein is.
From a different perspective, you can think of it as something that I’m going to call ‘an energy matrix,’ which is really a representation of the protein from the perspective of its function. What it tells you is how each position of the DNA that contacts the transcription factor shapes the binding between the two molecules. Using those types of matrices, you can model with much higher accuracy how a given protein will bind DNA. Also, you can better understand systems that are present and how they evolve. A lot of our work revolves around that. We make very large mutant libraries of binding sites of those transcription factors to know what those are, which is where NGS really comes in. It’s impossible to do any of that work without it. These are standard sequencing experiments using Fluorescence-Activated Cell Sorting (FACS) to split mutants based on their effect on gene expression level.
Q: As a teaser, what will you be sharing during your upcoming webinar with Azenta?
My goal is to help people understand the evolution of microbes and evolution in general: how we can study it, why it matters, and what we don’t know about it. I want to show how using interdisciplinary approaches can help us solve some of the ‘big problems’ like antimicrobial resistance, especially when it comes to how we can better predict evolution, as well as answer how regulation and evolution are connected.
Register to attend our free, one-hour webinar with Dr. Lagator to learn how he and his team strive to make evolutionary factors impacting bacterial resistance more predictable when developing novel drugs and treatments. A live Q&A with Dr. Lagator will follow.
About the Guest
Mato Lagator, Ph.D.
Dr. Mato Lagator carried out his undergraduate work at Harvard University and his Ph.D. at the University of Warwick, where he studied the evolution of resistance in Chlamydomonas reinhardtii. In 2013, Dr. Lagator started his postdoc at the Institute of Science and Technology Austria (ISTA) with Calin Guet and Jon Bollback, slowly defining his major research interest–the relationship between molecular biology and evolution.
Dr. Lagator joined Manchester University to start his own research group as a Presidential Fellow and has since transitioned onto a Wellcome Trust – Royal Society Sir Henry Dale Fellowship. His research group, currently consisting of two postdocs and four Ph.D. students, studies various aspects of gene regulatory evolution and antimicrobial resistance.