2014 NSF CAREER grant MCB Reviews
2015 NSF DEB Preproposal (with Britt Koskella) Reviews
Friday, January 23, 2015
Monday, January 19, 2015
My thoughts on "The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer"
I was on a late Christmas break last week, when I caught wind of a newly published study (here) and associated write ups (best one by Ed Yong here) which suggested that natural transformation and type VI secretion (T6S) were linked in Vibrio cholerae. Given my research interests into microbe-microbe interactions, and my experience studying and writing about natural transformation and evolution, I was naturally intrigued. I was also wary, however, because these kinds of studies tend to oversell correlations and tend towards "just so" stories. Having now read the paper a couple of times, I actually think it's quite a good example of a microbial genetics story and much less so evolutionary biology story.
I won't go into the gory details too much, but the authors start out pointing out that little is known about regulation of the T6S system in Vibrio. The main take home result of this paper is that the T6S system operons are controlled by TfoX and also by quorum sensing through HapR and QstR. That's a solid story and worthy of publication in a pretty high tier journal. However, due to a happenstance of history moreso than anything else, TfoX is also said to be a master regulator of competence for natural transformation in Vibrio. This association arose because TfoX was originally identified as a regulator of competence in the presence of chitin. Looking back in hindsight, maybe TfoX should be referred to as a master regulator of pathways associated with chitin presence.
The authors decide to run with with regulatory association between T6S and competence, and test whether killing of cells by T6S facilitates horizontal gene transfer through natural transformation. As a way to suggest that there is a more evolutionary link between these processes, the authors set up experiments to demonstrate that genetic exchange dependent on T6S killing can occur. For this experiment, the authors test for the ability of their focal T6S wielding strain to be transformed by a kanamycin resistance gene integrated into the genome of another Vibrio cholerae strain. Surprise, surprise (/sarcasm) the experiment works and T6S facilitates genetic exchange. <edit, that last sentence and the tone of this section aren't appropriate. I realize this now and apologize>. I say that snarkily because ANY process that releases DNA from cells can facilitate horizontal transfer by natural transformation...heat, lightning, whatever you can imagine. My problem here is that the authors place their finger on the scale to effectively rig an experiment whereby they will get the "sexy" result that would be undoubtedly overspun in press releases. The problem, and this goes for a lot of papers (especially of the microbiome sort) is that just because something is possible under experimental conditions doesn't make that phenomenon evolutionarily relevant. How did the authors bias this experiment and why am I annoyed enough to hastily craft a blog post?
1) Natural transformation frequency of genomic DNA is highly dependent on similarity of donor and recipient genomes. Transformation by plasmids is a bit different because these don't require recombination. The authors used two (relatively closely related) different Vibrio strains ensuring that recombination could occur. I doubt this experiment would have nearly the success rate (if at all) if different Vibrio species were used as prey. The chances of success fall with genomic divergence from the recipient strain. I have no clue of what the spectrum of other bacteria that live on planktonic crustaceans that would be killed by Vibrio, but the more diverse they are the less likely that T6S truly affects genetic exchange.
2) The type of selection matters. The authors set up the experiment with kanamycin resistance, because they can plate out strains onto antibiotics and strongly select for transformants. Not critiquing that part, and it's certainly how you'd do the experiment, but I'm not sure that such selective environments are representative life on crustaceans or in the ocean. For T6S to have evolved to significantly affect genetic exchange requires a constantly changing environment with strong selection pressures whereby prey strains can be more adapted than predator strains. To this point, laboratory experiments have begun to show that natural transformation can increase rates of adaptation, but generally only in "stressful" environments. It's possible that such conditions could consistently arise for Vibrio, but it's a hard sell.
3) Since T6S preferentially targets dissimilar strains, there is a much much much greater chance that transformation of DNA from prey cells would be detrimental than beneficial. Rosie Redfield has already made the case (here and here) that transformation of DNA from closely related strains is likely detrimental because transformable DNA will contain more deleterious alleles on average than living cells. Additionally, there is always the chance of incorporating alleles that lower the transformation rate and which can't easily be replaced once incorporated. Transformation of DNA from prey cells targeted by T6S systems introduces two related problems. Although transformable DNA won't inherently contain deleterious mutations (unlike Rosie's paper, cells are killed by other cells rather than by deleterious mutations) many of the genes within this pool will be diverged from those in the recipient genome. Therefore, it would be much (much much+++) more likely that predator cells would be transformed by alleles of housekeeping genes that wouldn't function efficiently when placed into a new genomic context than by beneficial genes (here although see here). Is it likely that Vibrio cells will grow equally well if you replace their copy of rpoD with that of Pseudomonas? Probably not. On average then, forgive the lack of a mathematical model but I could whip one up if you'd really like, it is probably much easier to lower fitness of Vibrio through transformation after killing by T6S than to increase fitness. Added to this, analogous to alleles that lower competence in Rosie's model, is that genes that render strains sensitive to killing by T6S will be overrepresented in the transformable DNA pool.
4) Last but not least...I can understand why authors and press releases would be spun to suggest a tight evolutionary link between T6S, competence, and genetic exchange. As Rosie has pointed out, it's a much cleaner evolutionary story to think that predator cells are killing prey for nutrition. Also see her comment on Ed's blog post (here). The authors chose to play up the genetic exchange angle rather than test whether DNA from killed cells could be used as a nutrient. They don't even mention that DNA (and proteins, and a bunch of other things from lysed cells) could be used as a nutrient even though they use the terms predator and prey. Now to bring everything full circle, TfoX is actually the ortholog of Sxy, the gene in Haemophilus influenzae that Rosie's nutrient research is focused on. C'mon folks, at least acknowledge the literature.
So in conclusion, it's a nice genetics story.
I won't go into the gory details too much, but the authors start out pointing out that little is known about regulation of the T6S system in Vibrio. The main take home result of this paper is that the T6S system operons are controlled by TfoX and also by quorum sensing through HapR and QstR. That's a solid story and worthy of publication in a pretty high tier journal. However, due to a happenstance of history moreso than anything else, TfoX is also said to be a master regulator of competence for natural transformation in Vibrio. This association arose because TfoX was originally identified as a regulator of competence in the presence of chitin. Looking back in hindsight, maybe TfoX should be referred to as a master regulator of pathways associated with chitin presence.
The authors decide to run with with regulatory association between T6S and competence, and test whether killing of cells by T6S facilitates horizontal gene transfer through natural transformation. As a way to suggest that there is a more evolutionary link between these processes, the authors set up experiments to demonstrate that genetic exchange dependent on T6S killing can occur. For this experiment, the authors test for the ability of their focal T6S wielding strain to be transformed by a kanamycin resistance gene integrated into the genome of another Vibrio cholerae strain. Surprise, surprise (/sarcasm) the experiment works and T6S facilitates genetic exchange. <edit, that last sentence and the tone of this section aren't appropriate. I realize this now and apologize>. I say that snarkily because ANY process that releases DNA from cells can facilitate horizontal transfer by natural transformation...heat, lightning, whatever you can imagine. My problem here is that the authors place their finger on the scale to effectively rig an experiment whereby they will get the "sexy" result that would be undoubtedly overspun in press releases. The problem, and this goes for a lot of papers (especially of the microbiome sort) is that just because something is possible under experimental conditions doesn't make that phenomenon evolutionarily relevant. How did the authors bias this experiment and why am I annoyed enough to hastily craft a blog post?
1) Natural transformation frequency of genomic DNA is highly dependent on similarity of donor and recipient genomes. Transformation by plasmids is a bit different because these don't require recombination. The authors used two (relatively closely related) different Vibrio strains ensuring that recombination could occur. I doubt this experiment would have nearly the success rate (if at all) if different Vibrio species were used as prey. The chances of success fall with genomic divergence from the recipient strain. I have no clue of what the spectrum of other bacteria that live on planktonic crustaceans that would be killed by Vibrio, but the more diverse they are the less likely that T6S truly affects genetic exchange.
2) The type of selection matters. The authors set up the experiment with kanamycin resistance, because they can plate out strains onto antibiotics and strongly select for transformants. Not critiquing that part, and it's certainly how you'd do the experiment, but I'm not sure that such selective environments are representative life on crustaceans or in the ocean. For T6S to have evolved to significantly affect genetic exchange requires a constantly changing environment with strong selection pressures whereby prey strains can be more adapted than predator strains. To this point, laboratory experiments have begun to show that natural transformation can increase rates of adaptation, but generally only in "stressful" environments. It's possible that such conditions could consistently arise for Vibrio, but it's a hard sell.
3) Since T6S preferentially targets dissimilar strains, there is a much much much greater chance that transformation of DNA from prey cells would be detrimental than beneficial. Rosie Redfield has already made the case (here and here) that transformation of DNA from closely related strains is likely detrimental because transformable DNA will contain more deleterious alleles on average than living cells. Additionally, there is always the chance of incorporating alleles that lower the transformation rate and which can't easily be replaced once incorporated. Transformation of DNA from prey cells targeted by T6S systems introduces two related problems. Although transformable DNA won't inherently contain deleterious mutations (unlike Rosie's paper, cells are killed by other cells rather than by deleterious mutations) many of the genes within this pool will be diverged from those in the recipient genome. Therefore, it would be much (much much+++) more likely that predator cells would be transformed by alleles of housekeeping genes that wouldn't function efficiently when placed into a new genomic context than by beneficial genes (here although see here). Is it likely that Vibrio cells will grow equally well if you replace their copy of rpoD with that of Pseudomonas? Probably not. On average then, forgive the lack of a mathematical model but I could whip one up if you'd really like, it is probably much easier to lower fitness of Vibrio through transformation after killing by T6S than to increase fitness. Added to this, analogous to alleles that lower competence in Rosie's model, is that genes that render strains sensitive to killing by T6S will be overrepresented in the transformable DNA pool.
4) Last but not least...I can understand why authors and press releases would be spun to suggest a tight evolutionary link between T6S, competence, and genetic exchange. As Rosie has pointed out, it's a much cleaner evolutionary story to think that predator cells are killing prey for nutrition. Also see her comment on Ed's blog post (here). The authors chose to play up the genetic exchange angle rather than test whether DNA from killed cells could be used as a nutrient. They don't even mention that DNA (and proteins, and a bunch of other things from lysed cells) could be used as a nutrient even though they use the terms predator and prey. Now to bring everything full circle, TfoX is actually the ortholog of Sxy, the gene in Haemophilus influenzae that Rosie's nutrient research is focused on. C'mon folks, at least acknowledge the literature.
So in conclusion, it's a nice genetics story.
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