What are a group of genes that help Mycobacterium tuberculosis infect mammalian cells doing in a harmless soil bacterium? Dr Paul Hoskisson explains his recent research, which is helping us understand the evolutionary roots of disease.
Scientists invest a lot of time and resources in trying to understand how bacteria cause disease. Generally, this involves studying a particular gene, or group of genes, in a pathogenic (disease-causing) bacterium to see what function it has during the infection process. In my laboratory, we have been trying to understand the evolutionary processes that cause these genes to develop.
Bacteria need some specialist skills if they’re going to cause disease: they must avoid being destroyed by the immune system, enter and multiply within host cells, and produce toxins. Bacteria have been around on Earth a lot longer than humans, which suggests that the genes needed to cause disease in humans have either evolved recently and rapidly (in evolutionary terms) or been co-opted from existing genes in harmless bacteria.
We noticed that the soil bacterium Streptomyces coelicolor has a cluster of genes that are very similar to pathogenicity genes present in Mycobacterium tuberculosis, the causative agent of tuberculosis. Other work has shown that these genes, known as mce (mammalian cell entry) genes, are used by M. tuberculosis to colonise and survive inside human immune cells called macrophages. We disrupted these genes in S. coelicolor to see what happened.
As the mce genes are used by M. tuberculosis to infect and survive in macrophages, we wanted to see what happened to the mce-deficient S. coelicolor mutants under similar conditions. However, because S. coelicolor lives in the soil, it rarely encounters any immune cells, so we had to get creative.
Rather than use immune cells, we used amoebae. This might not seem like an obvious choice, but these single-celled organisms are eukaryotic, just like immune cells, and engulf bacteria in a similar way. We got a strange result when we fed the S. coelicolor mce mutants to the amoebae: the amoebae all died (see image above). This effect has been seen in M. tuberculosis as well – mce mutants are hyper-virulent and much better at killing immune cells than regular M. tuberculosis. This is counterintuitive, but while the mutant M. tuberculosis strain may be excellent at killing macrophages, it is unable to cause disease in a whole animal – presumably because of the presence of the complete immune system, which is much more complex.
We did a little detective work and discovered that the mce genes encode a transporter that bacteria use to take up sterol (a type of fat), which they can use as a source of food, from the environment. It is thought that M. tuberculosis uses this transporter to take up sterols because other nutrients are hard to find inside macrophages.
One location where Streptomyces encounters sterols in the environment is around the roots of plants, an environment known as the rhizosphere. We showed that the S. coelicolor mce mutant is poorer at colonising plant roots than the wild-type S. coelicolor, which suggests that sterols are an important carbon source for these bacteria.
We suggest that as these bacterial species adapted to their particular environment – soil in the case of the Streptomyces and human immune cells for M. tuberculosis – their respective mce genes evolved to operate under the different conditions. Understanding how the selection process has led to the changes in function are essential to our appreciation of the evolution of virulence in bacteria and could significantly aid our understanding of the emergence of pathogenic bacterial strains.
Paul A Hoskisson is a lecturer in microbiology at the University of Strathclyde. His research focuses on antibiotic-producing actinomycetes and emerging actinomycete pathogens.
Image adapted from the original article published in Scientific Reports article under the Open Access license.
Clark LC et al. Mammalian cell entry genes in Streptomyces may provide clues to the evolution of bacterial virulence. Sci Rep 2013;3:1109. doi:10.1038/srep01109
Bacterial cells are surrounded by a highly cross-linked cell wall that has to be constantly broken down and remade as the cells get bigger. Since most bacteria reproduce by dividing the cell into two they also have to build a new bit of cell wall in the middle of the cell to make two daughter cells. In bacteria the FtsZ protein forms a Z ring to mark this site of cell division and all the other cell division proteins assemble on this Z ring and remodel the cell wall.
Despite this, it has been known for a long time that some bacteria can exist as L forms which have lost their cell wall. Even more amazing, these L-form bacteria don’t need FtsZ to divide and instead they just bud off membrane vesicles, some of which contain DNA and enough proteins to form a new cell.
Jeff Errington’s group in Newcastle recently made stable L forms of a bacterium called Bacillus subtilis, effectively reversing 3 billion years of evolution . These bacteria can live without a wall or FtsZ but they still need a cell membrane to contain the cell contents and in another groundbreaking paper Jeff’s group have shown that simply increasing the amount of membrane the cell makes is enough to make these L-forms divide.
The beauty of these L forms is that they help us to understand how the first living cells, reproduced themselves around 4 billion years ago. In the absence of a cell wall and a complicated cell division machinery they simply increased their surface area to volume ratio in order to propagate. And that, frankly, is amazing.
Mercier R, Kawai Y and Errington J (2013). Excess membrane synthesis drives a primitive mode of cell proliferation. Cell 152 997-1007.
Image credit: The Red Lexicon on Wikimedia Commons
Posted by Matt Hutchings
This isn’t a research blog as such, just an attempt to get everyone to read a new perspective article entitled “Animals in a bacterial world”. Here at microbelog we’ve been banging on about how important symbioses between bacteria and eukaryotes are for a quite a while now. So imagine our excitement to read this article in the latest issue of the Proceedings of the National Academy of Sciences USA. Although slightly evangelical (or as one of my evolutionary biologist colleagues put it “messianic”), this is well worth a read. It’s also good to see Carl Woese and Lynn Margulis, both of whom sadly passed away recently, getting the credit they deserve. Facts like one third of human DNA is bacterial in origin is the kind of thing that gets us very excited! This is a call to arms and it’s certainly never been a more exciting time to be a microbiologist!
Image credit: Picture of a captive leaf-cutter ant colony taken by Andrew Smith, John Innes Centre, Norwich 2012.
Recently, I found a paper published in mBIO that describes how antibiotic use in farming is involved in the spread of resistance genes. In this case the work focuses on the humble honeybee (Apis mellifera). Since the 1950s, beekeepers in the USA have been using the antibiotic oxytetracycline – a ‘broad-spectrum’ antibiotic that kills most species of bacteria – to prevent infections that can cause ‘foul brood’, a disease that kills bee larvae. As you can imagine, using a single antibiotic for more than 50 years has led to some selective pressure. In this work, researchers from Yale University were investigating the prevalence of disease resistance in bee gut bacteria.
This might seem like a strange place to look, but it actually has its advantages. Unlike the supremely complex ecosystem of the human gut microbiome, the bee’s is pretty simple, with eight species making up over 95% of the gut bacteria in adult worker bees. The small number of species and the knowledge of how hives have been treated allowed the researchers to monitor the impact of decades of antibiotic use.
Sometimes you find a paper with a title so intriguing you just have to find out a little more about it. Recently, I came across a paper about ‘entombed pigs’, so how could I possibly ignore it? I learned a fair bit about animal-disease control methods in Asia and the use of quicklime to decompose corpses , a fairly standard weekend for me.
The work centres on foot-and-mouth disease (FMD), a viral infection of hoofed animals caused by Aphthovirus. It causes significant suffering in animals and has serious economic consequences: a 2001 outbreak is estimated to have cost the UK £8 billion.
Millions of infected animals were culled in South Korea in 2010/11, then buried (rather than burnt, as they are in the UK). The slaughtered animals were placed in five-metre-deep pits and covered with quicklime and copious amounts of soil to prevent the FMD spreading. Problem solved? Well, perhaps not.
A recent study led by Professor Tracy Palmer at the University of Dundee discovered a new way by which bacteria can insert proteins into membranes, using two different transport machines. Here she gives us the lowdown on what it’s all about…
All cells are surrounded by lipid membranes; they keep the insides in, and the outsides out, but sometimes bacteria need to bring a molecule from the environment into the cell, or vice versa. The membrane itself is pretty much impermeable, so the cell uses specialised proteins to make channels in the membrane so they can control what moves from one side to the other.
Imaging technologies have come a long way since the invention of the microscope 400 or so years ago. Now we can look at the circulatory system in a developing chicken embryo or the hair cells on a terrapin’s inner ear, but there’s one very familiar place that remains a mystery: the inside of a plant pot.
There’s a good reason why it would be great to have a peek into the peat – to learn what’s going on between the plant roots and soil-dwelling microbes in situ (something we’ve written about before). These interactions are environmentally and economically important, and many have been intensely studied. The symbiosis between rhizobia and plant roots allows nitrogen fixing, and many pathogens, such as fungi of the genus Phytophthora, use roots as a route into a plant.
So what’s stopping us looking at the roots? The answer’s fairly obvious: you can’t see through soil. You can overcome this hurdle by using non-optical imaging techniques such as MRI to look at root structures, much as you can use them to see inside your head – but they can’t pick up light emitted by fluorescent proteins, for example.
I read a short paper this week that is making early inroads into another option: make soil see-through. Well, not soil precisely, but lumps of Nafion – a polymer invented in the 1960s that’s used in fuel cells. By grinding the Nafion down, researchers in Scotland have made it into particles similar to those found in soil.
Nafion isn’t normally see-through, but it has a refractive index very close to that of water. What that means in practice is that when you add water, the polymer disappears (this video shows something similar).
The Nafion particles that have been produced aren’t totally identical to soil, but they’ve been altered to have similar water and nutrient availability. It seems to work: plant growth in the transparent soil is comparable to growth in the real thing.
The researchers have already visualised GFP-labelled E. coli O157:H7 colonising the roots of lettuce seedlings. This bacterium, which is an important human pathogen, can grow quite happily on salad vegetables. The above picture is from the paper, showing the fluorescent E. coli on the lettuce roots.
This demonstrates how useful this technology could become. Although the authors concede that it’s not perfect for every type of plant–microbe interaction, there’s so much we don’t know about life in the loam that any insights we can get should advance both plant science and microbiology significantly.
Downie H, Holden N, Otten W, Spiers AJ, Valentine TA, & Dupuy LX (2012). Transparent soil for imaging the rhizosphere. PloS one, 7 (9) PMID: 22984484