Study Guide

Prokaryotes Themes

  • Evolution

    A remarkable thing about how quickly bacteria grow is that it is possible to see evolution happen on a really fast time scale. Prokaryotes adapt to their environment by two main methods

    1. Swapping DNA with other prokaryotes

    2. Accumulating mutations in the DNA they already have

    We’re going to talk about how antibiotic resistance can evolve by each of these methods, and then we’re going to discuss using evolution as a tool for biotechnology.

    Antibiotic Resistance from Exchanging Genes

    Tetracycline is an antibiotic. In case you’re wondering, it’s a bacteriostatic antibiotic that works by inhibiting protein synthesis. Tetracycline resistance typically develops by bacterial expression of proteins that transport the antibiotic outside of cells. Antibiotic resistance that depends upon an exporter typically depends upon sharing of genes between strains since evolving a whole new transporter is hard.

    Antibiotic Resistance from Genomic Mutation

    Streptomycin is antibiotic that, like tetracycline, inhibits protein synthesis. Streptomycin resistance, however, typically follows a different route. A shift in one amino acid in a ribosomal protein can completely protect bacteria from streptomycin activity. All cells, including bacterial cells, occasionally make slightly imperfect copies of their DNA which leads to shifts in proteins. Streptomycin resistance typically comes from a mutation in the gene that encodes this specific ribosomal protein.

    Evolution and Biotechnology

    Evolution and spread of antibiotic resistance is worrisome, and we will talk about that more in the Real Worldsection. Evolution in bacteria can be used to perform useful tasks, however. In a process called directed evolution, natural selection can be used to make microbes do new, useful things for us.

    Directed evolution might work like this. Let’s say we had a bacterial strain that turned bright green whenever iron was around. Imagine this activity depended upon a protein called IroN, produced from the gene iroN. But maybe we don’t care about iron, maybe we're more interested in lead. And you’d be right to be worried about lead levels; lead is quite toxic to humans. So a bacterium that can indicate lead levels might be a very useful thing to have around.

    If we wanted to make a bacterial test for lead levels, we could expose the bacteria to lead and just wait. Eventually a strain that turned green in response to lead might develop. But we might have to wait a really long time. One way you could help the bacteria evolve is to help them mutate. Brief exposure to X-rays or UV light or to various hazardous chemicals can lead to much higher mutation rates in DNA. This is a reasonable route, and is done in lots of situations.

    We're in a better situation here, though. We already know that these bacteria produce a response to iron that depends in the iroN gene, which makes the IroN protein. We can get mutant copies of the iroN gene by PCRing the gene with a special DNA polymerase, called an error-prone polymerase, that makes a lot of mistakes while copying the gene.

    After you have mutant versions of iroN , you can clone and insert in into a plasmid. This plasmid is transformed into bacterial cells just like we transformed bacteria with SUPER APE. All you need to do next is grow bacteria containing different iroN mutants and look for those that turn green in response to lead exposure.

    We talked about testing for lead above, but you could look for a number of things. You could find bacteria that can grow in high levels of oil (to be used in cleaning up oil spills). Or maybe you work for a company that produces the amino acid cysteine, and you want to develop bacteria that make even more of it. Or, finally, maybe you want to develop bacteria that can "smell" chocolate cake. Umm, we’re not sure why, but you might.

    We can try to evolve bacteria that can do any of these things. Selecting for bacteria that grow in high levels of oil might be more like looking for a streptomycin mutant. We could grow bacteria, perhaps after mutating their genomes broadly, in oil and look for those bacteria that survive.

    If we wanted to find bacteria that could produce more cysteine, or those that can smell chocolate cake, you might want to start by mutating genes that make the proteins that produce cysteine or mutate genes that sense umm something that’s sort of similar to chocolate cake. Good luck with that last one. But we bet you could get the cysteine idea to work.

    Check out this cartoon.

  • Levels of Organization

    While multicellular animals and plants like humans and sunflowers are clearly complicated, organized groups of cells, we often think of each bacterial cell as behaving independently. Sometimes, however, bacterial cells do work together to make organized structures.

    Intraspecies Levels of Organization

    We talked earlier about biofilms, which are communities of microbial cells, and how spores, which are dormant, protected bacteria. While some bacteria sporulate in planktonic form, others, notable myxobacteria, produce organized cell structures that help disseminate their spores. Consider the two images below.

    Image from here.

    The image to the left shows different bacterial structures called fruiting bodies. Fruiting bodies are kind of a bacterial version of a sunflower. The bacterial cells come together to develop into structures with spores on the top, ripe for spreading. The image to the right is a microscope image of several fruiting bodies produced by colonies of the mycobacterium Myxococcus xanthus.

    Interspecies Levels of Organization

    Many scientists study the populations of bacteria that develop on your teeth every morning. They are complex mixes of cells that land in a predetermined order every night. Some bacteria are really good at sticking to your teeth directly; the next species is good at sticking to those initial bacteria, and so on. This is organization on a mixed-species level.

  • Unity and Diversity

    One of the major themes in biology is how we can be really alike in lots of ways and really different in others. For example, we share a huge amount of our DNA with mice, and in lots of ways we’re similar, but in lots of ways we’re really different too. One way in which humans are all kind of the same, but also a little different from each other is in the population of microflora, the microbes that live in and on us all.

    As we talked about earlier, our guts are full of microbes that are digesting the bits of food we can’t digest ourselves. In return for this food supply, these microbes are making some useful vitamins for us. The same thing is going on in other mammals, including mice. By and large humans and mice have some of the same types of bacterial strains resident in them. But, relatively small, shifts in bacterial populations among different humans and among different mice can have outcomes on traits including weight.

    Our guts contain high numbers of bacteria from two bacterial phyla, the Bacteroidetes, which are Gram-negative, and Firmicutes, which are Gram-positive. Scientists observed that obese humans had a higher percentage of Firmicutes relative to Bacteroidetes than leaner humans did.
    Firmicutes are a little better at making use of the extra food going through the intestines than the Bacteroidetes bacteria are.

    It makes sense that obese individuals’ microbiota might be better at getting extra energy from food. Since the bacteria are making compounds that get used by their human hosts, humans harboring extra Firmicutes might indeed be expected to have more weight. What wasn’t clear was which came first, the obese human, or the fattening bacteria. In order to investigate, scientists at Washington University in Saint Louis looked at similar bacteria in normal and obese mice. If you’ve never seen an obese mouse, here you go:

    What these scientists saw was that the normal and obese mice had the same shifts in Bacteroidetes relative to Firmicutes that humans had. They were then able to do an experiment.

    In the first step, they took some bacteria from both obese and lean mice. Then, they got some "germ-free mice" that didn’t have any bacteria in their guts at all. They inoculated the germ-free mice with the bacteria from either obese or lean mice and studied the development of the (formerly) germ-free mice. They saw that mice inoculated with bacteria from the obese mice became fatter than mice that had gotten bacteria from leaner mice.

    These experiments underline how even though we all have, similar types of bacteria in our system small differences can lead to noticeable changes.