New research into the toxins, virulence, spread and prevention of the superbug Clostridium difficile is reported in the June special issue of the Journal of Medical Microbiology. These findings will play a crucial role in providing us with ammunition in the fight against a sometimes deadly pathogen.

Clostridium difficile is found in the environment but is most common in hospitals. It can cause a serious hospital-acquired infection when antibiotics are used as they upset the balance of the normal gut flora, allowing C. difficile to grow and produce toxins. It is carried in the guts of 3% of healthy humans but carriage rates in hospital patients tend to be much higher and elderly people in hospitals, being treated with antibiotics are most at risk of developing infection. The bacteria produce spores when they encounter unfavourable conditions. Transmission of infection is through the ingestion of these spores which can survive on surfaces and floors for years and are resistant to many disinfectants and antiseptics, including alcohol hand gel.

Symptoms include diarrhoea, nausea, abdominal pain, loss of appetite, fever, bowel inflammation and possible perforation, which can be fatal. Only two antibiotics are regularly used to treat C. difficile infection: metronidazole and vancomycin, but relapse is a common problem following treatment. In 2004, a hypervirulent strain (C. difficile 027/NAP1/BI) was reported, which appears to make toxins more rapidly and at higher levels than other strains, as well as being resistant to many antibiotics, including fluoroquinolones.

Several studies in the Journal of Medical Microbiology look at the spread of C. difficile in different countries, including Austria and Korea. Research shows that the use of antibiotic increased the risk of outbreaks of the hypervirulent strain of C. difficile in the Netherlands. The issue also contains evidence to suggest that C. difficile could be spread between animals and humans – researchers have isolated the bacterium from food animals in Slovenia.

Scientists investigated the effects of antibiotics, antigens and other agents on the virulence and pathogenicity of C. difficile. Toxins were also studied; research reveals some important information about the synthesis, processing and effects of different toxins. A new gene sequence has been discovered in the hypervirulent C. difficile 027 strain, which could be related to its increased virulence by affecting toxin binding.

The potential for a ‘designer’ probiotic for C. difficile is discussed. Professor Ian Poxton, former Editor-in-Chief of the Journal of Medical Microbiology said “this is an important approach that is hopefully much better than previously reported studies using commercially available yoghurt-like drinks, and certainly more palatable than ‘faecal transplants’.”

Big pharma gave up on soil bacteria as a source of antibiotics too soon, according to research published in the June issue of Microbiology. Scientists have been mining microbial genomes for new natural products that may have applications in the treatment of MRSA and cancer and have made some exciting discoveries.

“Over the last eight years we have been looking for new natural products in the DNA sequence of the antibiotic-producing bacterium Streptomyces coelicolor,” said Professor Gregory Challis from the University of Warwick. “In the last 15 years it became accepted that no new natural products remained to be discovered from these bacteria. Our work shows this widely-held view to be incorrect.”

In 1928 Alexander Fleming discovered penicillin, which was subsequently developed into a medicine by Florey and Chain in the 1940s. The antibiotic was hailed as a ‘miracle cure’ and a golden age of drug discovery followed. However, frequent rediscovery of known natural products and technical challenges forced pharmaceutical companies to retreat and stop looking for new molecules.

Currently the complete genetic sequences of more than 580 microbes are known. It is possible to identify pathways that produce new compounds by looking at the DNA sequences and many gene clusters likely to encode natural products have been analysed. ‘Genome mining’ has become a dynamic and rapidly advancing field.

Professor Challis and his colleagues have discovered the products of two cryptic gene clusters. One of the clusters was found to produce several compounds that inhibit the proliferation of certain bacteria. Three of these compounds were new ones, named isogermicidin A, B and C. “This discovery was quite unexpected,” said Professor Challis. “Our research provides important new methodology for the discovery of new natural products with applications in medicine, such as combating MRSA infections.”

The other product they discovered is called coelichelin. Iron is essential for the growth of nearly all micro-organisms. Although it is the fourth most abundant element in the Earth’s crust it often exists in a ferric form, which microbes are unable to use. “The gene cluster that directs production of coelicehlin was not known to be involved in the production of any known products,” said Professor Challis. “Our research suggests that coelichelin helps S. coelicolor take up iron.”

Many researchers have followed Professor Challis and his colleagues into the exciting field of genome mining. “In the near future, compounds with useful biological activities will be patented and progressed into clinical or agricultural trials, depending on their applications” said Professor Challis.

US researchers have created ‘living computers’ by genetically altering bacteria. The findings of the research, published in BioMed Central’s open access Journal of Biological Engineering, demonstrate that computing in living cells is feasible, opening the door to a number of applications including data storage and as a tool for manipulating genes for genetic engineering.

A research team from the biology and the mathematics departments of Davidson College, North Carolina and Missouri Western State University, Missouri, USA added genes to Escherichia coli bacteria, creating bacterial computers able to solve a classic mathematical puzzle, known as the burnt pancake problem.

The burnt pancake problem involves a stack of pancakes of different sizes, each of which has a golden and a burnt side. The aim is to sort the stack so the largest pancake is on the bottom and all pancakes are golden side up. Each flip reverses the order and the orientation (i.e. which side of the pancake is facing up) of one or several consecutive pancakes. The aim is to stack them properly in the fewest number of flips.

In this experiment, the researchers used fragments of DNA as the pancakes. They added genes from a different type of bacterium to enable the E. coli to flip the DNA ‘pancakes’. They also included a gene that made the bacteria resistant to an antibiotic, but only when the DNA fragments had been flipped into the correct order. The time required to reach the mathematical solution in the bugs reflects the minimum number of flips needed to solve the burnt pancake problem.

“The system offers several potential advantages over conventional computers” says lead researcher, Karmella Haynes. “A single flask can hold billions of bacteria, each of which could potentially contain several copies of the DNA used for computing. These ‘bacterial computers’ could act in parallel with each other, meaning that solutions could potentially be reached quicker than with conventional computers, using less space and at a lower cost.” In addition to parallelism, bacterial computing also has the potential to utilize repair mechanisms and, of course, can evolve after repeated use.

A naturally occurring molecule made by symbiotic gut bacteria may offer a new type of treatment for inflammatory bowel disease, according to scientists at the California Institute of Technology.”Most people tend to think of bacteria as insidious organisms that only make us sick,” says Sarkis K. Mazmanian, an assistant professor of biology at Caltech, whose laboratory examines the symbiotic relationship between “good” bacteria and their mammalian hosts. Instead, he says, “bacteria can be beneficial and actively promote health.”

For example, the 100 trillion bacteria occupying the human gut have evolved along with the human digestive and immune systems for millions of years. Some harmful microbes are responsible for infection and acute disease, while “other bacteria, the more intelligent ones, have taken the evolutionary route of shaping their environment by positively interacting with the host immune system to promote health, which gives them an improved place to live; it’s like creating bacterial nirvana,” says Mazmanian.

If bacteria are actively modifying the gut, their work would have to be mediated by molecules. In their recent work, Mazmanian and his colleagues have identified one such molecule, a sugar called polysaccharide A, or PSA, which is produced by the symbiotic gut bacterium Bacteroides fragilis. They have termed this molecule a “symbiosis factor,” and predict that many other bacterial compounds with diverse beneficial activities await discovery.

To identify the molecule and its action, the scientists used experimental mice and induced changes to their intestinal bacteria by exposing them to a pathogenic bacterium called Helicobacter hepaticus. This microbe causes a disease in the mice that is similar to Crohn’s disease and ulcerative colitis. However, when the animals were co-colonized with B. fragilis, they were protected from the disease–as were animals that were given oral doses of just the PSA molecule.

In particular, Mazmanian and his colleagues found that PSA induced particular immune-system cells called CD4+ T cells to produce interleukin-10 (IL-10), a molecule that has previously been shown to suppress inflammation–and offer protection from inflammatory bowel disease. “Thus, bacteria help reprogram our own immune system to promote health,” he says.

“The most immediate and obvious implication is that PSA may potentially be developed as a natural therapeutic for inflammatory bowel disease,” says Mazmanian.

Inflammatory bowel disease, a constellation of illnesses that cause inflammation in the intestines, including ulcerative colitis and Crohn’s disease, is estimated to affect one million Americans. The rates of inflammatory bowel diseases have skyrocketed in recent years; for example, the incidence of Crohn’s disease, a condition that causes debilitating pain, diarrhea, and other gastrointestinal symptoms, has increased by 400 percent over the past 20 years.

The current research, along with other work by Mazmanian and June L. Round, a Caltech postdoctoral researcher, suggests that the interplay between various groups of bacteria living in the intestines has profound effects on human health.

This notion gels with the so-called “hygiene hypothesis.” The hypothesis, first proposed two decades ago, links modern practices like sanitation, vaccination, a Western diet, and antibiotic use, which reduce bacterial infections, to the increased prevalence of a variety of illnesses in the developed world, including inflammatory bowel disease, asthma, multiple sclerosis, and Type 1 diabetes. However, it is now clear that increased living standards and antibacterial drugs affect not only infectious microbes, but all of the beneficial ones that we may depend on for our well-being.

“Through societal measures we have changed our association with the microbial world in a very short time span. We don’t have the same contact with microbes as we have for millions of years–we just live too clean now,” Mazmanian says. So while it is useful to eliminate disease-causing organisms, “perhaps disease results from the absence of beneficial bacteria and their good effects,” he suggests. “This study is the first demonstration of that. What it hopefully will do is allow people to re-evaluate our opinions of bacteria. Not all are bad and some, maybe many, are beneficial.”

Life in outer space is an absolute certainty, and it is likely to be more familiar than we might think, according to an article in the May issue of Microbiology Today. Ever since the start of the space race we have sent more than just satellites and astronauts into space: spacecraft are not routinely decontaminated and are teeming with microbial life.

“Wherever man boldly goes his microbial fauna is sure to follow,” said Lewis Dartnell, an astrobiologist at University College London. The Russian space station Mir was launched in 1986 and microbial studies investigated the diversity of bacteria living alongside the astronauts. In 1998, free-floating blobs of water found during a NASA mission to the station were analyzed and discovered to contain microbes including faecal bacteria like E. coli, plague bacterium-related species of Yersinia, and even what was suspected to be Legionella, as well as fungi, amoebae and protozoa.

“Preventing the spread of microbial life between worlds of the solar system has been a top priority for decades now,” said Lewis. “This effort is known as planetary protection.” Today’s International Space Station (ISS) is much cleaner than Mir was 20 years ago, thanks to HEPA filters, weekly cleaning and biweekly disinfecting regimes. But inevitably, the ISS is still far from being bug-free; recent sampling revealed the bacterium Staphylococcus epidermidis surviving in different areas.

But it’s not just planets we need to protect – astronauts are at increased risk of infection in space. Respiratory infections are common among astronauts and diseases occur in a quarter of space shuttle flights. “Prolonged exposure to cosmic radiation and microgravity is believed to have a negative effect on the immune system, and disease transmission is enhanced within the closed environment of recycled air and water,” said Lewis Dartnell. Microbes also pose an increased risk of allergies, toxic air and water supply and even biodegradation of critical spacecraft components.

This week, the Phoenix lander touched down on Mars, hoping to take the first ever direct measurements of Martian water and organic molecules. “To guarantee the cleanliness of the robotic arm, it was enclosed in a biobarrier bag – effectively an interplanetary condom,” said Lewis. But this will not be a feasible control measure for humans. “Humans and spaceships are inherently dirty and once we arrive to plant flags in the rusty soil our microbial entourage will begin leaking out onto Mars.” What’s more, microbes have an uncanny ability to survive as spores, resistant to heat, cold and radiation. “Once humans have visited Mars, we may never be certain that any biological discoveries weren’t simply signs of our own dirty sleeves,” said Lewis Dartnell.

In fact, we might actually need to take microbes on a manned mission to Mars. “For longer missions, it will not be possible to take sufficient supplies from Earth,” said Lewis. “Scientists are developing ingenious life support systems relying on plants and micro-organisms to provide food, waste recycling and water purification.” Of course, in this case, an outbreak of harmful microbes could crash life support systems as well as affecting the health of the crew, endangering the whole mission. “For better or worse, space bugs are here to stay.”

Ships are inadvertently carrying trillions of stowaways in the water held in their ballast tanks. When the water is pumped out, invasive species could be released into new environments. Disease-causing microbes could also be released, posing a risk to public health, according to an article in the May issue of Microbiology Today.

“There is no romantic adventure or skullduggery at work here,” said Professor Fred Dobbs from Old Dominion University, Virginia, USA. Ships pump water in and out of ballast tanks to adjust the waterline and compensate for cargo loading, making the ship run as efficiently as possible. These tanks can hold thousands of tonnes of water. “Any organisms in the water are likely to be released when it is next pumped out.”

Many non-native animals and plants have been taken to new environments and become invasive, threatening the survival of local species; some fundamentally alter the ecosystem. Zebra mussels were introduced in North America and the comb jelly in the Black Sea and both have had enormous ecological and economic impacts

For more than 20 years we have known that a variety of large phytoplankton and protozoa are transported in this way, but we know very little about smaller microbes like bacteria and viruses. “It is inevitable that hundreds of trillions of micro-organisms enter a single ship’s ballast tank during normal operations,” said Professor Dobbs. The majority of these microbes are harmless, but some are a potential risk to public health.

“Vibrio cholerae, which causes cholera in humans, can be carried in ballast tanks,” said Professor Dobbs. “There have been no known outbreaks of disease associated with ballasting activities, but the water is only sampled very rarely.” Other disease-causing microbes in the tanks include Cryptosporidium parvum and Giardia duodenalis, which cause stomach upsets.

Some people say microbes are present everywhere; they may be easily dispersed because they are so small. However, many experts believe micro-organisms have a “biogeography”, a natural home, which means they could become invasive if moved and have a negative effect on different environments. There is some evidence for this argument: two phytoplankton species called diatoms were introduced to the English Channel from the North Pacific Ocean

The International Maritime Organisation, which sets rules and standards for the global shipping industry, has proposed an upper limit to the numbers of Vibrio cholerae, E. coli, and intestinal enterococci contained in discharged ballast water. A few ships are also using different treatments to reduce and even eliminate the microbes in their ballast water. “A number of techniques are being looked at for this purpose, from filtration to biocides, ultrasound to ultraviolet irradiation,” said Professor Dobbs. “Our understanding of the issues involved will increase as more studies are carried out, particularly those employing the tools of modern molecular biology.”

Researchers from the John Innes Centre and the University of East Anglia have recently elucidated the structure and function of an enzyme which is involved in decorating antibiotics with sugar molecules. Many antibiotics have a variety of different carbohydrate molecules attached to them which can help the antibiotic to be taken up by the target organism or overcome resistance. By manipulating the sugar, it may be possible to restore usefulness in antibiotics to which resistance has developed.

The aim of this research was to find out how these sugars are made, and how their structures affect their biological activity. The researchers studied an enzyme from a little studied species of Streptomyces bacteria, which produces the antibiotic tylosin. The enzyme they looked at is involved in making a sugar molecule that decorates tylosin. By working out how the carbohydrates are made, it may be possible to make unnatural sugars, with different properties.

“This is a bit of biochemistry we can’t do with chemistry. We need to go back to the fundamentals of how these sugars are put together in nature”, said Professor Rob Field. “We want to see what happens when we decorate an antibiotic with sugar and which sugars make the best decoration.”

They are not yet near to a market product, but trying to understand at a fundamental level how these sugars are made. “We are still putting the toolkit together” said Professor Field. By modelling the enzyme, and comparing it with related enzymes, they have been able to identify the key parts needed for its function, and propose the biochemical basis for how it creates the carbohydrate’s precise st

Once considered a barren plain with the odd hydrothermal vent, the seafloor appears to be teeming with microbial life, according to a paper being published May 29 in Nature.

“A 60,000 kilometer seam of basalt is exposed along the mid-ocean ridge spreading system, representing potentially the largest surface area for microbes to colonize on Earth,” said USC geomicrobiologist Katrina Edwards, the study’s corresponding author.

While seafloor microbes have been detected before, this is the first time they have been quantified.  Using genetic analysis, Edwards and colleagues found thousands of times more bacteria on the seafloor than in the water above.

Surprised by the abundance, the scientists tested another Pacific site and arrived at consistent results.  This makes it likely that rich microbial life extends across the ocean floor, Edwards said.

The scientists also found higher microbial diversity on the rocks compared with other vibrant systems, such as those found at hydrothermal vents.

Even compared with the microbial diversity of farm soil—viewed by many as the richest—diversity on the basalt is statistically equivalent.

“These scientists used modern molecular methods to quantify the diversity of microbes in remote deep-sea environments,” said David L. Garrison, director of the National Science Foundation’s biological oceanography program.

“As a result, we now know that there are many more such microbes than anyone had guessed,” he added.

These findings raise the question of where these bacteria find their energy.

“We scratched our heads about what was supporting this high level of growth when the organic carbon content is pretty darn low,” Edwards recalled.

With evidence that the oceanic crust supports more bacteria compared with overlying water, the scientists hypothesized that reactions with the rocks themselves might offer fuel for life.

Back in the lab, they calculated how much biomass could theoretically be supported by chemical reactions with the basalt.  They then compared this figure to the actual biomass measured.  “It was completely consistent,” Edwards said.

This lends support to the idea that bacteria survive on energy from the crust, a process that could affect our knowledge about the deep-sea carbon cycle and even evolution.

For example, many scientists believe that shallow water, not deep water, cradled the planet’s first life.  They reason that the dark carbon-poor depths appear to offer little energy, and rich environments like hydrothermal vents are relatively sparse.

But the newfound abundance of seafloor microbes makes it theoretically possible that early life thrived—and maybe even began—on the seafloor.

“Some might even favor the deep ocean for the emergence of life since it was a bastion of stability compared with the surface, which was constantly being blasted by comets and other objects,” Edwards suggested.

Still, current knowledge of the deep biosphere can fit on the head of a pin, Edwards said.  Most seafloor bacteria uncovered in this study show little relation to those cultivated in labs, which makes experimentation difficult.

Rather than bringing bacteria to the lab, however, Edwards plans to bring the lab to bacteria—with a microbial observatory 15,000 feet below sea level.

Thanks to a $3.9-million grant awarded in March by the Gordon and Betty Moore Foundation, Edwards and over 30 colleagues will continue studying seafloor bacteria, but will also study their subseafloor cousins that cycle through the porous rock.

The first expedition of its kind, the drilling operation will penetrate 100 meters of sediments and 500 meters of bedrock.

Besides experiments aimed at learning how precisely these bacteria alter rock, the scientists will measure the diversity, abundance and relatedness of microbes at different depths.

This will shed light on whether the bacteria evolved from ancestors that floated down from above or from some as yet unknown source deep in the crust.

The Nature study provides a crucial base of comparison between the seafloor and subseafloor microbes, both completely unknown until just recently.

The decade-long undertaking will further bridge the earth and life sciences, a key goal in the emerging field of geobiology, described by Edwards as the co-evolution of Earth and life.

The deep biosphere is uniquely suited for a geobiological approach, Edwards said, since a proper understanding requires genomics, analysis of microbe-rock chemical interactions and a timescale in the millions of years.

Edwards joined USC two years ago as part of its cluster hire of scientists with multidisciplinary interests related to geobiology.  With its concentration of faculty in the field, Southern California and USC in particular are regarded as hubs for the geobiology research community.

USC recently hosted the 5th Annual Geobiology Symposium, co-organized by USC post-doctoral student Beth Orcutt, the second author of the Nature paper.

In addition, the USC Wrigley Institute for Environmental Studies runs a summer geobiology course on Catalina Island that brings together top students and faculty.

Edwards believes that most people just don’t realize how much life thrives in the watery depths.

“If we can really nail down what’s going on, then there are significant implications,” she said.  “It is my hope that people turn their heads and notice that there’s life down there.”

Scientists search for drug candidates in some very unlikely places. Not only do they churn out synthetic compounds in industrial-scale laboratories, but they also scour coral reefs and scrape tree bark in the hope of stumbling upon an unsuspecting molecule that just might turn into next year’s big block buster. But one region that scientists have not been searching is their guts. Literally.Now, a team of researchers at Harvard Medical School, Brigham and Women’s Hospital, and the California Institute of Technology have demonstrated that a molecule produced by bacteria in the gut’s intestinal microflora can eliminate symptoms of inflammatory bowel disease (IBD), a condition that includes Crohn’s disease and ulcerative colitis, in animal models.

“Given the sheer number of bacteria in the gut, the potential for discovering new molecules that can treat a whole range of these diseases is promising,” says Dennis Kasper, co-lead author on the study, professor of medicine and microbiology and molecular genetics at Harvard Medical School, and director of the Channing Laboratory at Brigham and Women’s Hospital.

The study will appear as the cover story in the May 29 issue of Nature.

Scientists have known for many decades that the mammalian gut is an ecosystem teeming with approximately 1,000 different species of bacteria, species as distinct from the host as a single-cell amoeba in pond scum. Rather than causing disease, these bacteria are responsible for protecting against infection and aiding digestion. An increasing number of scientists also suspect that recent increases in asthma and even certain food allergies are caused by disruptions in the delicate balance of this intestinal ecosystem.

In 2005, Kasper and Sarkis Mazmanian, then a postdoc in Kasper’s lab and now an assistant professor of biology at the California Institute of Technology, discovered that a species of intestinal bacteria called Bacteroides fragilis could restore immune system balance in mice that were bred to lack intestinal bacteria. A particular product of B. fragilis, a sugar molecule called polysaccharide A (PSA), recovered the equilibrium of a certain subclass of immune system cells (called Th1 and Th2) whose levels became skewed when bacteria in the gut were absent. The researchers referred to PSA as a “symbiosis factor,” one that established a beneficial link between bacteria and mammals. This was the first study in which such a link was demonstrated.

Interestingly, when the study was completed, Kasper and Mazmanian found in these mice an abundance of immune system cells that were known to protect against colitis and Crohn’s disease. In the current report, the groups decided to expand these findings and explore potential links between PSA and inflammatory bowel disease.

When immunocompromised mice with a specific pathogen-free microbiota were given an intestinal bacterium called Helicobacter hepaticus, they soon developed “rip roaring” IBD, according to Kasper. However, when Helicobacter was combined with B. fragilis, the mice were fine. Further experiments revealed that PSA—the special sugar molecule—was the key factor in preventing IBD. In fact, when mice were given Helicobacter combined with PSA purified from B. fragilis bacteria, they showed no symptoms of IBD.

“But then the key question was, if PSA was essential for preventing these animals from coming down with either colitis or Crohn’s, how did it do it”” says Kasper. “What was the mechanism””

The answer came by studying a subset of interleukins, that is, molecules secreted by immune cells.

Previous studies had shown that two particular interleukins, called IL-17 and IL-23, promote intestinal inflammation and are present at high levels in IBD patients. Here, while the researchers found IL-17 and IL-23 in the guts of animals who had received Heliobacter alone, these interleukins were absent from animals who had also received both PSA-producing B. fragilis and purified PSA.

“We realized that something in PSA must be preventing the inflammation that causes colitis and Crohn’s, which would explain the reduction in IL-17 and IL-23,” says Kasper.

This hunch brought the researchers to consider a third interleukin, IL-10. The opposite of IL-17 and IL-23, IL-10 is anti-inflammatory and had previously been shown to protect against experimental colitis.

The researchers once again administered Helicobacter and PSA-active B. fragilis (the combination that had previously led to healthy mice), only this time they included an antibody that blocked IL-10. As a result, the mice all came down with IBD.

“This demonstrated for us the mechanism by which PSA protects against IBD,” says Kasper.

Indeed, the researchers deduced that PSA prompts immune system cells to secrete IL-10, which in turn suppresses the inflammation caused by IBD. In other words, PSA is an anti-inflammatory.

This research should encourage people (including many scientists) to consider the vast potential for beneficial contributions to human health by “good” bacteria. And what’s more, “This is the first time that a beneficial molecule produced by intestinal bacteria has been shown to work therapeutically in an animal model,” says Mazmanian.

The researchers caution that these findings do not promise any near-term treatments for IBD. “PSA might do the same thing in humans, and it might not,” says Kasper.

However, the mechanism that they’ve discovered should persuade scientists and drug manufacturers to consider new sources for expanding the drug pipeline.

“There is currently no effort to develop molecules that are naturally made by bacteria to use therapeutically,” continues Mazmanian. “This study opens up that possibility.”

Full citation:
Nature, May 29, 2008, 453 (7195), 620-624
“A microbial symbiosis factor prevents intestinal inflammatory disease”
Sarkis K. Mazmanian(1), June L. Round(1) & Dennis L. Kasper(2,3)

A group of Duke University researchers have made a major advance in understanding how bacteria divide.  These results could lead to new antibiotic treatments that prevent dangerous bacteria from multiplying.

Normally, bacteria divide by forming a ring that pinches the cell in two.  The ring is called a “Z ring” after the protein FtsZ, which forms a ring-shaped scaffold and then squeezes it smaller.  In bacteria, the Z ring also contains a dozen other proteins, all believed to be essential for division.

The Z ring normally pulls in on the cell membrane by binding to another protein, FtsA, which has one end attached to the inner cell membrane and the other end connected to FtsZ.  When the Z ring constricts, it completely pulls in the membrane and nips the bacterium in two.

But cell biology research scientist Masaki Osawa, Ph.D., cut FtsA out of the system by making an FtsZ that could bind directly to the membrane, and called it “membrane targeted FtsZ” or FtsZ-mts.

First, Osawa demonstrated that the new protein, FtsZ-mts, assembled Z rings in bacteria.

Then he constructed a greatly simplified cell-division machine in microscopic oil droplets, called liposomes, that demonstrated the important role of FtsZ in the division process.  He was able to assemble Z rings in this completely artificial system, the liposome, a tiny hollow sphere of fat that mimics natural cell membranes.

To do this, Osawa mixed the liposomes with FtsZ and GTP, a molecule that provides energy.  On a microscope slide the liposomes fused and stretched into tubes that mimicked the shape of E. coli and other rod-shaped bacteria.

“It was a happy coincidence that the size and shape of the liposomes was similar to that of rod-shaped bacteria,” says co-author Harold Erickson, professor of cell biology.  “These tubular liposomes are a new micro-structure, and their formation is still a mystery.”

During the experiment, fluorescently labeled FtsZ-mts was initially on the outside of the liposomes, but some of the tubular liposomes ended up with FtsZ on the inside.  “We don’t know how this happens, but it is a key to the discovery,” Osawa said.

Inside the liposome the FtsZ formed multiple closed rings that aligned perpendicular to the length of the tube, just as Z rings form in bacteria.  They also slid back and forth, and where they collided, they stayed together and formed brighter Z rings.  And as the Z rings grew in brightness, they visibly pulled the wall of the liposome inward.

“The Z rings are clearly generating force and causing the constriction,” Osawa said.  A movie the team made shows several constrictions in the wall occurring at the sites of the bright Z rings.  When the GTP in the liposome is used up, the tube eases out of its constrictions into its original shape.

“We believe our simple system may recreate the mechanism that the earliest bacteria used to divide.  They probably had FtsZ alone,” Erickson said.  “Osawa’s experiments show that FtsZ, a membrane tether, and the inside surface of a tubular membrane are all that’s needed to assemble the Z ring and generate a constriction force.”

The artificial Z rings were not sufficient to pinch the liposomes in half, “probably because their walls are much thicker than the membrane of a bacterium,” Osawa noted.  “We are now working to make thinner liposomes, so that we can achieve complete division.”

Erickson said that FtsZ is the bacterial ancestor of tubulin, the protein that makes the microtubules in animal cells and is the target of a number of anti-cancer drugs like taxol.  Although FtsZ is not sensitive to taxol, anything learned about the bacterial ancestor will help us understand microtubules, which help animal cells to keep their shape and control their movements, he explained.

Alex Dajkovic, lead author on the paper and a former postdoctoral fellow at Johns Hopkins. He is now a researcher at Institut Curie in Paris.

A research team from Johns Hopkins has solved important puzzles concerning how certain proteins guide the reproduction of bacteria, discoveries that could lead to a new type of antibiotics.

In a recent study published in the journal Current Biology, the scientists reported how a belt-like structure called a Z ring, which pinches a rod-shaped bacterium to produce two offspring, can be disabled by a protein called MinC. By exploiting this vulnerability, the researchers said, pharmaceutical companies may find a way to fight infections that no longer respond to older medications.

“The potential medical applications of our discovery are significant,” said Alex Dajkovic, lead author of the paper. “Because the molecules involved in cell division are very similar in almost all bacteria, the process we uncovered provides a new target for the people who make antibiotics. This is extremely important because antibiotic resistance is on the rise, and many preventable deaths, especially in the developing world, are caused by bacterial infections.”

Denis Wirtz, professor of chemical and biomolecular engineering at Johns Hopkins.

Dajkovic helped make the discoveries as a postdoctoral fellow in the lab of Denis Wirtz, a professor of chemical and biomolecular engineering in Johns Hopkins’ Whiting School of Engineering. Dajkovic is now a researcher at Institut Curie in Paris.

Wirtz, who also is associate director of the Johns Hopkins Institute for NanoBioTechnology, noted that “most antibiotics target the ability of bacteria to build their cell walls or their ability to make proteins or DNA. With this paper, Alex and the rest of the team identified new molecular targets that could disrupt bacterial cell division. If the bacteria can’t reproduce, the infection will die.”

The researchers focused on the rod-shaped bacterium E. coli, commonly found in the human digestive tract, which serves as a model organism for study of basic bacterial processes. When these single-celled microbes want to multiply, a structure called the Z ring forms, then begins to tighten like a rubber band around each bacterium’s midsection. The Z ring helps to pinch the rod-shaped body into two microbial sausages that finally split apart to form two cells.

For about 20 years, researchers have known about the Z ring but have not understood precisely how it operated and why it always formed in the middle of rod-shaped cells. The main components of Z rings are filaments of a protein molecule called FtsZ

In the new journal article, the Johns Hopkins-led researchers were able to report for the first time that the changing of FtsZ threads from a liquid-like form to a more solid structure inside the cell is important for the formation of the Z ring. The team found that FtsZ threads weave themselves into a framework or scaffold that can hold all of the other molecules involved in the cell division process. The FtsZ filments are able to weave this tapestry, the researchers learned, because they tend to attract one another and interact along the length of each thread.

The team also discovered that MinC, another protein inside the bacterial cell, disrupts this process by liquefying the structure that is used to form a Z ring. “MinC blocks the attraction between FtsZ filaments along their lengths, and it also makes the filaments more fragile,” said Dajkovic. “This has the effect of shearing the weavings in the tapestry of the Z ring, which causes the whole structure to fall apart.”

MinC is most prevalent on the outer ends of the rod-shaped bacterial cell, the researchers said, and this explains why the Z ring always forms and splits the cell in the middle, where it is less likely to encounter its protein foe. The team members said this discovery also presents a promising opportunity: a new drug that mimics the effects of MinC could play havoc with the bacterial reproductive process and thereby put an end to an infection.

The findings resulted from a collaboration involving Dajkovic, whose background is in cell biology and biochemistry; Wirtz, whose expertise is in biophysics and engineering; and Sean X. Sun, a Johns Hopkins assistant professor of mechanical engineering who provided computational modeling of the cell division process. Wirtz and Sun were co-authors of the Current Biology paper, along with Ganhui Lan, a doctoral student in Sun’s lab, and Joe Lutkenhaus, a University Distinguished Professor in the Department of Microbiology, Molecular Genetics and Immunology at the University of Kansas Medical Center. Lutkenhaus was Dajkovic’s faculty advisor as a doctoral student.

Today, scientists know more now than ever before about the microbes that inhabit our mouths. They know so much, in fact, that gathering all of the relevant bits of information into one place when designing experiments can be a job in itself. Now, grantees of the National Institute of Dental and Craniofacial Research (NIDCR), part of the National Institutes of Health, and their international colleagues intend to solve this problem with the launch of the first comprehensive database of the oral microbiome, or the approximately 600 distinct microorganisms currently known to live in the mouth.The free online compendium is called the Human Oral Microbiome Database (HOMD). The database goes live today as the digital equivalent of an Oxford dictionary of oral microorganisms, providing detailed biological entries for each species and an extensive catalogue of the thousands of genes that these microbes express. The site is located at http://www.homd.org and is overseen by scientists at The Forsyth Institute in Boston and King’s College London in England.

“The HOMD fills a critical research need,” said NIDCR director Lawrence Tabak, D.D.S., Ph.D. “The oral microbiome is extremely rich in data, and HOMD becomes the essential search engine for scientists to view and retrieve this information, generate novel hypotheses, make computational discoveries, and ultimately develop more biologically sound therapies to control oral diseases.”

According to Floyd Dewhirst, D.D.S., Ph.D., a leader of the project and a scientist at The Forsyth Institute, HOMD also introduces the first comprehensive nomenclature system to bring order to the naming of uncultured or previously unnamed oral microbes. The standardized numbering system helps to eliminate the Babel of confusing names and uninformative database designations that have frustrated scientists and sometimes hindered their research.

The database also categorizes each microbe by its 16S rRNA sequence, a distinctive fingerprint of genetic information that scientists have used for the past two decades to identify microorganisms. This sequence information allows the microbes to be placed in a family tree that shows how they are related to one another. For those organisms whose DNA has been sequenced, HOMD provides online tools to view and analyze all of their genes and proteins. Each category of information in the database is interlinked, readily searchable, appropriately annotated, and will be frequently updated to remain current.

Dewhirst noted that although HOMD has officially opened to scientists, the database remains an ongoing project. “We’ve already assembled a great deal of useful information for the research community, but we will continue to expand and refine the database for the next several years,” said Dewhirst. “I can see the Human Oral Microbiome Database serving as a valuable model for other microbiome databases now and in the years to come.”

Informally called “biology’s next revolution,” microbiome studies have opened a needed window into the complex microbial communities that occupy most parts of the human body. These studies will define how microbes contribute to sustaining health and, when their community dynamics are perturbed, play a role in common chronic disease, such as tooth decay and periodontal disease in the mouth. In December 2007, NIH launched the Human Microbiome Project that initially will sequence all of the genes, or genomes, of 600 representative microorganisms sampled from microbial communities in the mouth, skin, digestive tract, nose, and female urogenital tract. Additional studies are either under way or under development.

Among those already well under way is a NIDCR-supported project to compile a full catalogue of the complete genomes of all oral microbes. It has generated a tremendous amount of data and, coupled with the decades of more traditional studies of oral bacteria, the need for a comprehensive, user-friendly database has become a priority.

“The oral microbiome is currently better understood than those of other sites in the body, such as the intestine,” said Dr. Bruce Paster, Ph.D., also at The Forsyth Institute and another project scientist. “Since oral microorganisms appear in infections throughout the human body, the HOMD database certainly will be useful to physicians. Likewise, microbiologists in industry will find HOMD helpful because oral microbes sometimes contaminate food or the drug manufacturing process.”

The National Institute of Dental and Craniofacial Research (NIDCR) is the Nation’s leading funder of research on oral, dental, and craniofacial health.

Bacteria can be used to engineer genetic modifications, thereby providing scientists with a tool to combat many challenges in areas from food production to drug discovery. However, this sophisticated technology can also be used maliciously, raising the threat of engineered pathogens. New research published in the online open access journal Genome Biology shows that computational tools could become a vital resource for detecting rogue genetically engineered bacteria in environmental samples.Jonathan Allen, Shea Gardner and Tom Slezak of the Lawrence Livermore National Laboratory in California, US, designed new computational tools that identify a set of DNA markers that can distinguish between artificial vector sequences and natural DNA sequences. Natural plasmids and artificial vector sequences have much in common, but these new tools show the potential to achieve high sensitivity and specificity, even when detecting previously unsequenced vectors in microarray-based bioassays.

A new computational genomics tool was developed to compare all available sequenced artificial vectors with available natural sequences, including plasmids and chromosomes, from bacteria and viruses. The tool clusters the artificial vector sequences into different subgroups based on shared sequence; these shared sequences were then compared with the natural plasmid and chromosomal sequence information so as to find regions that are unique to the artificial vectors. Nearly all the artificial vector sequences had one or more unique regions. Short stretches of these unique regions are termed ‘candidate DNA signatures’ and can be used as probes for detecting an artificial vector sequence in the presence of natural sequences using a microarray. Further tests showed that subgroups of candidate DNA signatures are far more likely to match unseen artificial than natural sequences.

The authors say that the next step is to see whether a bioassay design using DNA signatures on microarrays can spot genetically modified DNA in a sample containing a mixture of natural and modified bacteria. The scientific community will need to cooperate with computational experts to sequence and track available vector sequences if DNA signatures are to be used successfully to support detection and deterrence against malicious genetic engineering applications. Scientists would be able to maintain an expanding database of DNA signatures to track all sequenced vectors.

“As with any attempt to counter malicious use of technology, detecting genetic engineering in microbes will be an immense challenge that requires many different tools and continual effort,” says Allen.

References

1. DNA signatures for detecting genetic engineering in bacteria
Jonathan E Allen, Shea N Gardner and Tom R Slezak
Genome Biology (in press)

Article available here:
http://genomebiology.com/imedia/1534720787156665_article.pdf?random=277103