Saturday Cimema: How mushrooms can save the world

Yeast shows what drives cells to divide

Mitochondria have been found to also be the driver with regard to cell division, according to a group of biochemists who say this discovery could play a large role in finding cures for many human diseases. The scientists studied yeast cells and found that mitochondria, which generate 90 percent of the cell’s energy, can be the deciding factor behind how fast cells divide. The finding by Michael Polymenis and Mary Bryk and their research groups is published today in the open-access journal PLoS Genetics. The finding changes the traditional view of the mitochondrion from an “energy depot” at the service of its larger cellular host to a “command center” that directs cell division. The researchers used regular baker’s yeast (Saccharomyces cerevisiae) - commonly used in bread, wine and beer making - because many of the yeast cell’s processes are similar to those in human cells. From unicellular yeast to complex mammals, the process is the same. The job of a cell is to divide and grow. Metabolism takes in “food” and turns it into fuel and building blocks for DNA replication and gene expression. But when these processes falter, diseases can result. Too much cell division too quickly, for example, is typical of cancerous cells. Conversely, poor metabolism - stemming from mitochondrial deficiencies - is at the root of damage to various organs such as the brain, heart, skeletal muscles, and liver. All of the body processes that require a lot of energy are impacted by this, and at least 1 in every 4,000 people worldwide suffer from mitochondrial deficiencies that result in problems with normal development, motor control, vision, hearing, or liver and kidney function. Alternatively, there are times when speeding cell division might be useful as with wound healing and plant or crop production. If we can understand the basic pathway that regulates cell division, we can think of ways to tweak the different steps in that path with therapeutics to help people who have problems with these high-energy organs. The research showed that when a yeast cell’s mitochondria decided to “turn on the switch,” the cell’s nucleus, which carries most of the genetic material, received the message and cell division began. So now we need to connect that link. We need to understand how and when the mitochondria send the message. If we know how the message is sent, we might be able to control it.

Coordination between cellular metabolism and DNA replication determines when cells initiate division. It has been assumed that metabolism only plays a permissive role in cell division. While blocking metabolism arrests cell division, it is not known whether an up-regulation of metabolic reactions accelerates cell cycle transitions. Here, we show that increasing the amount of mitochondrial DNA accelerates overall cell proliferation and promotes nuclear DNA replication, in a nutrientdependent manner. The Sir2p NAD+-dependent de-acetylase antagonizes this mitochondrial role. We found that cells with increased mitochondrial DNA have reduced Sir2p levels bound at origins of DNA replication in the nucleus, accompanied with increased levels of K9, K14-acetylated histone H3 at those origins. Our results demonstrate an active role of mitochondrial processes in the control of cell division. They also suggest that cellular metabolism may impact on chromatin modifications to regulate the activity of origins of DNA replication.
An Increase in Mitochondrial DNA Promotes Nuclear DNA Replication in Yeast. 2008 PLoS Genet 4(4): e1000047

Evolution of root nodule symbiosis with nitrogen-fixing bacteria

Nitrogen is essential for all plants and animals, but despite being surrounded by an element that constitutes 79% of air, only a few bacteria can absorb it directly from the environment. All other species are ultimately dependent on these microbes as a source. A new paper in the open-access journal PLoS Biology investigates the genetics behind the symbiotic relationship between these nitrogen-fixing bacteria and plants, and presents evidence of specific genetic changes that might have led to the evolution of symbioses with nitrogen-fixing bacteria from a more ancient form of symbiosis.

About 80% of all land plants have a symbiotic relationship with fungi of the phylum Glomeromycota. The fungus penetrates cells in the plant s roots, and provides the plant with phosphates and other nutrients from the soil. This kind of symbiosis is called an arbuscular mycorrhiza, and evolved more than 400 million years ago. Professor Martin Parniske and colleagues started their study by looking at genes known to be involved in arbuscular mycorrhiza, to see whether they could find evidence of any specific genetic differences in plants that form symbioses also with nitrogen-fixing bacteria. In this so-called root nodule symbiosis bacteria live in the root cells of the host plants, where they bind elementary nitrogen from the air in special organs, the nodules. In return, the microbes get high-energy carbohydrates produced by photosynthesis in the host plant.

It had already been speculated that genes involved in the arbuscular mycorrhiza symbiosis might have been recruited for nodulation, as these symbioses both involve intracellular relationships. One clue was that several genes, including the so-called symbiosis-receptor-kinase-gene (SYMRK), are involved in a genetic program that links arbuscular mycorrhiza and one form of bacterial nodule symbiosis. This work is an important step towards understanding the evolution of nitrogen-fixation in plants, and even whether plants that don’t form symbioses with nitrogen-fixing bacteria could be engineered to do so, thus increasing their nutritional value.

Functional adaptation of a plant receptor-kinase paved the way for the evolution of intracellular root symbioses with bacteria. 2008 PLoS Biol 6 (3): e68.

MicrobiologyBytes 2007: Year in Review

2007 has been a record breaking year for MicrobiologyBytes, so here’s a look back at some of the highlights:

We started January off with noroviruses and ancient plague, then relaxed a bit by playing with Lego and brewing beer.

In February, we looked at yaws and Mimivirus, then went green by reducing our carbon footprint with microdiesel.

And in March we marked World Tuberculosis Day by looking at new drugs for an old foe.

April started off with an exploration of whether viruses evolve to protect their hosts, then we took out first look at colony collapse disorder affecting bees.

May was dominated by news about extreme drug resistant tuberculosis (XDR-TB) and chikungunya, then later looked at probiotics.

In June we looked at the origins of yellow fever and quorum sensing in Serratia (quorum sensing remains one of the most popular topics on MicrobiologyBytes).

July began with flesh eating bacteria and finished up with prions and Alzheimers disease.

In August, most people took a holiday and this was the quietest month of the year in terms of visitors, but we still managed to fit in Hendra, chikungunya and Marburg viruses.

September brought lots of bad news for UK farmers, so we looked at the biology of the bluetongue and foot and mouth disease virus outbreaks in the UK.

In October we covered the bacterial SOS system and debated the strategy for HPV vaccination in the UK.

November started with the terrorist threat posed by glanders and melioidosis then considered the dangers of Chlamydia infection and the opportunities presented by DNA microarrays.

We finished up the year with bacteriocins and bacterial morphology.

Phew. Overall, the most popular posts of the year were:

1. Hepatitis C Virus: a mountain to climb
2. Fungal Infections and All About Fungi
3. Infectobesity
4. Toll-Like Receptors
5. DNA microarrays

See you next year!

Salamander skin bacteria fight chytrid fungus

Beneficial bacteria that live on salamander skins have the ability to inhibit pathogenic fungi. Our study aimed to identify the specific chemical agents of this process and asked if any of the antifungal compounds known to operate in analogous plant-bacteria-fungi systems were present. Crude extracts of bacteria isolated from salamander skin were analyzed. These investigations show that 2,4-diacetylphloroglucinol is produced by the bacteria isolate Lysobacter gummosus, which was found on the red-backed salamander, Plethodon cinereus. Furthermore, exposure of the amphibian fungal pathogen, Batrachochytrium dendrobatidis, to different concentrations of 2,4-diacetylphloroglucinol resulted in an IC₅₀ value comparable to crude extract concentrations. This study is the first to show that an epibiotic bacterium on an amphibian species produces a chemical that inhibits pathogenic fungi.

The Identification of 2,4-diacetylphloroglucinol as an Antifungal Metabolite Produced by Cutaneous Bacteria of the Salamander Plethodon cinereus. J Chem Ecol. 2007, Dec 6

Related:

• Chytrid fungus
• Fungus fighter
• Frogs vs Bacteria

Peer Reviewed: Latest publications

Polar Exploration

The spatial organization of bacterial cells is quite complex with proteins and protein complexes localized to specific subcellular regions. However, the mechanisms by which asymmetric proteins are localized are mostly unresolved. A variety of mechanisms are utilized to achieve polarity in bacteria. This article focusses on recent findings that support specific mechanisms for the establishment of polarity in rod shaped bacteria.
Several models by which polarity is achieved have been proposed. These include direct localization of the protein to the cell pole, random insertion followed by diffusion and capture at the pole, targeting to the site of cell division before septation. Variation on these general themes appears to be the rule rather than the exception, resulting in a wide variety of different mechanisms to achieve a seemingly similar goal - the specific positioning of a protein or protein complex to the cell pole. The emerging theme is that there is no one mechanism that governs polarity.

Polar explorations: Recent insights into the polarity of bacterial proteins.
Curr Opin Microbiol. 2007 Nov 12

Gamma interferon and fungal infections

In the first half of the 20th century, fungal infections were considered exotic diseases. This article in the Society for General Microbiology magazine Microbiology Today shows how this has changed and where interferon fits in.

Neutrophils, macrophages and dendritic cells are the first effector cells contacting fungal cells. Neutrophils are rapidly recruited to the site of infection and play an essential role in fungal killing. The presence of fungal cells and host effector cells initiates a cascade of events through both non-specific and specific mechanisms of host response. Lymphocytes T helper 1 (Th1), a CD4+ subset, are the predominant response to infections by invasive fungi, and cytokines associated with the Th1 phenotype, including interleukin (IL)-12, IL-8 and IFN-gamma, are critical to protective responses to the infection. Conversely the Th2-phenotype cytokines IL-4 and IL-10 contribute to the progression of the infection. Effector mechanisms of IFN-gamma and its role in modulating the host response against fungi include stimulation of macrophage and neutrophil killing of fungi by enhancement of both oxidative and non-oxidative mechanisms.

Bad Hair Day

Dandruff is an easily recognizable skin flaking condition occurring in up to 95% of humans. The presence of Malassezia species is not sufficient to cause either dandruff or the more extreme skin conditions - many people harbor Malassezia without showing symptoms. However, Malassezia must have an essential role in these conditions, because scalp flaking symptoms are improved by treatment with a variety of antifungal materials that remove Malassezia. Malassezia are also thought to contribute to the common skin disease atopic eczema by host sensitization to fungal protein allergens. Malassezia species are closely related to plant pathogens, implying an ancestral shift from plant to animal host preference. The M. globosa genome is among the smallest of genomes of free-living fungi.

Abstract: Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g. lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex.

Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. PNAS USA November 13, 2007

New insights into a polyphageous pathogen

Botrytis cinerea is an ascomycete responsible for gray mould on hundreds of dicot plants. In grapevines, conidia can contaminate leaves or inflorescences, but the fungus develops mainly in the autumn on ripe grapes. The wide variety of symptoms on different organs and plants may suggest that B. cinerea has a large arsenal of weapons to attack its host plants. This necrotrophic ascomycete displays the capacity to kill host cells through the production of toxins, reactive oxygen species and the induction of a plant-produced oxidative burst. Through an arsenal of degrading enzymes, B. cinerea is able to feed on different plant tissues. Recent molecular approaches show that this fungus shares conserved virulence factors with other phytopathogens, but also highlight some Botrytis-specific features. The discovery of some first strain-specific virulence factors, together with population data, even suggests a possible host adaptation of the strains. The availability of the genome sequence now stimulates the development of high-throughput functional analysis to decipher the mechanisms involved in the large host range of this species.
Botrytis cinerea virulence factors: new insights into a necrotrophic and polyphageous pathogen
FEMS Microbiology Letters 05 Oct 2007

Candida parapsilosis secreted lipase is a major virulence factor

Candida parapsilosis is the second most common cause of invasive candidiasis worldwide. This fungus is particularly associated with disease in premature infants and immunocompromised adults and is a major cause of infections in intensive care units. Despite increasing clinical importance, little is known about the genetic basis of fungal virulence traits that enable C. parapsilosis to cause disease. Virulence factors of C. parapsilosis need to be identified in order to develop more effective therapy against this pathogen. The authors developed a gene deletion system for C. parapsilosis and used it to delete the lipase locus in the C. parapsilosis genome. They also reconstructed the missing genes, which restored lipase activity. Biofilm formation was inhibited with lipase-negative mutants and their growth was significantly reduced in lipid-rich media. The knockout mutants were more efficiently ingested and killed by macrophage-like cells. Additionally, the lipase-negative mutants were significantly less virulent in infection models that involve inoculation of reconstituted human oral epithelium or murine intraperitoneal challenge. These studies represent the first targeted disruption of a gene in C. parapsilosis and show that C. parapsilosis-secreted lipase is involved in disease pathogenesis. This system for targeted gene deletion holds great promise for rapidly enhancing our knowledge of the biology and virulence of this increasingly common invasive fungal pathogen.

Targeted gene deletion in Candida parapsilosis demonstrates the role of secreted lipase in virulence.
J Clin Invest. 2007 Sep 13