Bacteriophages are among the smallest but most abundant organisms on earth. For most phages, the tail mediates the anchoring of the phage to generally abundant bacterial outer membrane proteins that serve as specific receptors for their substrates. For example, the receptor for the temperate phage λ is the Escherichia coli maltoporin receptor LamB, which functions in amylomaltose uptake. The establishment of a stable phage–host interaction relays signals that allow injection of DNA from the phage capsid through the tail and into the host, leaving the empty capsid (head) attached to the cell surface. Following phage λ DNA injection, a decision between the lytic or lysogenic pathways of bacteriophage λ is made. The poles (ends) of bacterial calls have specialized functions related to the mobilization of DNA and certain proteins. To monitor the infection of Escherichia coli cells by light microscopy, scientists developed procedures for the tagging of mature bacteriophages with quantum dots:
Surprisingly, most of the infecting phages were found attached to the bacterial poles. This was true for a number of temperate and virulent phages of E. coli that use widely different receptors and for phages infecting Yersinia pseudotuberculosis and Vibrio cholerae. The infecting phages colocalized with the polar protein marker IcsA–GFP. ManY, an E. coli protein that is required for phage λ DNA injection, was found to localize to the bacterial poles as well. Furthermore, labelling of λ DNA during infection revealed that it is injected and replicated at the polar region of infection. The evolutionary benefits that lead to this remarkable preference for polar infections may be related to λ’s developmental decision as well as to the function of poles in the ability of bacterial cells to communicate with their environment and in gene regulation.
By labelling different phages with quantum dots and following adsorption using a fluorescence microscope the researchers were able to investigate the initial steps of binding (adsorption) and phage DNA injection. The surprising results showed that at low multiplicities of infection, phages preferentially adsorb, inject and replicate their DNA at the bacterial poles. This spatial preference was independent of host proteins, ManY and Pel, required for phage λ DNA injection. The significance of the pole, the binding of the phage to the pole and its implications in lytic-lysogenic decision are discussed in the paper.
Magnetic or “magnetotactic” bacteria were first discovered in the 1960s, and naturally organize themselves in the direction of Earth’s magnetic field, as shown in this video:
Inside these bacteria there is a row of iron-containing crystals aligned with the long axis of the cell, giving them the equivalent of an internal magnetic compass needle (Molecular mechanisms of magnetosome formation. Ann Rev Biochem 2007 76: 351-66). Such bacteria can sense and align themselves relative to the earth’s magnetic field. Magnetotactic bacteria are major constituents of many natural microbial communities, especially in aquatic habitats. There is a broad range of shapes and groups of magnetic bacteria. However, cultivation of these organisms in the laboratory is often difficult and only few strains of magnetotactic bacteria have been isolated in pure culture, a tiny minority of the vast diversity of naturally occurring populations from largely unexplored natural habitats such as the marine environment.
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So why would bacteria want to be magnetic? Leaving aside the possibility that they are magnetic by accident, e.g. as a consequence of some metabolic byproduct, the truth is that we really don’t know the reason. However, the most likely explanation lies not in north-south alignment, but in up and down. The magnetotactic bacteria we know about require low but very precise levels of oxygen to survive, and must live in sediments where the oxygen concentration is just right for their needs. Over much of the globe, the Earth’s magnetic field actually points down towards the centre of the planet, so by following these lines of magnetic flux, they are able to ensure that they bury themselves in the sediment, which is exactly where they want to be. Thus the majority of magnetotactic in the Northern Hemisphere are north seeking, and those in the Southern Hemisphere are south seeking.
Diarrhoea is one of the leading infectious causes of death worldwide with an estimated 1.8 million deaths annually, primarily in young children in developing countries. There are many known causes of diarrhoea; however, the causes of up to 40% of the cases are still unknown. One possibility is that viruses that we currently do not know about are responsible for these cases. The advent of metagenomic sequencing has enabled systematic and unbiased characterization of microbial populations; thus, metagenomic approaches have the potential to define the spectrum of viruses, including novel viruses, present in stool during episodes of acute diarrhoea. The detection of novel or unexpected viruses would then enable investigations to assess whether these agents play a causal role in human diarrhoea.
This paper uses an experimental strategy termed “micro-mass sequencing” to systematically identify viruses present in stool from a number of patients suffering from diarrhoea. Using this methodology we detected known enteric viruses as well as multiple sequences from putatively novel viruses with only limited sequence similarity to viruses in GenBank. Sequences from a number of novel viruses were detected, some which differed quite significantly from any previously described virus. These new viruses may or may not be responsible for causing diarrhoea. Future studies will specifically address the potential of these viruses to cause human disease. One implication of this study is that there are likely to be many more unknown viruses that can be identified in this fashion. Furthermore, by studying these viruses, we will come to a more complete understanding of the role viruses play in diarrhoea. Ultimately, this may lead to the development of therapeutics and/or vaccines that decrease the disease burden of diarrhoea.
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.
The quality and safety of food products are among the most important factors influencing consumer choices in modern times, as well as being important considerations of food manufacturers and distributors. It is therefore of importance for the food industry to continue to seek out more effective methods to reduce undesirable changes in foods associated with food processing, such as loss of colour, flavour, texture, smell and, most importantly, nutritional value. High-pressure processing (HPP), is a relatively new, nonthermal food processing method that subjects foods (liquid or solid) to pressures between 50 and 1000 MPa. HPP treatment of food dates back over a century. Over the last 20 years, significant advances in HPP technology have been made, in the form of semi-continuous systems to the scaling up of pilot units to successful commercially viable processes.
HPP is a nonthermal process capable of inactivating and eliminating pathogenic and food spoilage microorganisms. This novel technology has enormous potential in the food industry, controlling food spoilage, improving food safety and extending product shelf life while retaining the characteristics of fresh, preservative-free, minimally processed foods. As with other food processing methods, such as thermal processing, HPP has somewhat limited applications as it cannot be universally applied to all food types, such as some dairy and animal products and shelf-stable low-acid foods. This article discusses the effects of high-pressure processing on microbial food safety and, to a lesser degree, food quality.
Radionuclides in the environment are one of the major concerns to human health and ecotoxicology. The explosion at the Chernobyl nuclear power plant renewed interest in the role played by fungi in mediating radionuclide movement in ecosystems. As a result of these studies, our knowledge of the importance of fungi, especially in their mycorrhizal habit, in long-term accumulation of radionuclides, transfer up the food chain and regulation of accumulation by their host plants was increased. Micro-fungi have been found to be highly resilient to exposure to ionizing radiation, with fungi having been isolated from within and around the Chernobyl plant. Radioresistance of some fungal species has been linked to the presence of melanin, which has been shown to have emerging properties of acting as an energy transporter for metabolism and has been implicated in enhancing hyphal growth and directed growth of sensitized hyphae towards sources of radiation. Using this recently acquired knowledge, we may be in a better position to suggest the use of fungi in bioremediation of radioactively contaminated sites and cleanup of industrial effluent.
Fungi appear to be very resistant to radionuclides in the environment. Part of this resistance may be the smaller amount of DNA per nucleus than mammalian cells, but evidence from comparative studies between pigment and nonpigmented fungi suggest there may be other factors that confer radioresistance. Melanin pigment may provide some protection against ionizing radiation and be integral to the absorption and retention of radionuclides. Owing to the long-lived and extensive hyphal network and biomass in upper soil horizons of forest ecosystems, fungi are very efficient in absorbing radionuclides, and are an important component of long term accumulation of radionuclides. This may be why radionuclide adsorption/desorption models do not conform to observed patterns, as mycorrhizal fungi mediate soil-to-plant transfer rates. Internal translocation of radionuclides to and hyper-accumulation into harvestable fruit bodies of macro-fungi has potential for environmental remediation but needs further evaluation.
Some estimates put total the worldwide economic damage due to plant viruses as high as US$60 billion per year, in addition to the human costs in terms of hunger and poverty. So understanding how viruses damage plants and how this can be avoided is of the utmost importance. There are hundreds of plant-pathogenic viruses, which cause a range of diseases. However, plants have evolved elaborate and effective defence mechanisms to prevent or limit virus damage. Plants contain resistance (R) genes, which allow resistance to a range of pathogens including viruses. Each R gene gives resistance to a particular pathogen. A number of R genes have been studied in detail (Mechanisms of plant resistance to viruses. 2005 Nature Reviews Microbiology 3: 789-798). Several molecules and signalling pathways are induced on pathogen recognition, and they cooperate to produce a defensive response. Some of the best characterized of these molecules include salicylic acid, nitric oxide and reactive oxygen species, in addition to some plant hormones. RNA silencing is a highly conserved pathway in animals and plants that functions in development and in the maintenance of genome integrity. Plants have adapted this system for antiviral defences, and of course, plant viruses have in turn developed mechanisms to suppress RNA silencing. Double-stranded RNA (dsRNA) is the trigger for RNA silencing. Most plant viruses (59 of the 80-odd plant virus genera) are RNA viruses and plants have several homologues of the DICER endonuclease. These enzymes generate siRNA (short interfering RNA) as an antiviral response. So these two pathways - RNA silencing and R-gene-mediated resistance - interact to produce an effective defence response in plants.
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Having penetrated the plant cell wall, the first defence mechanism which viruses encounter are extracellular surface receptors on the host cell plasma membrane that recognize pathogen-associated molecular patterns (PAMPs). This interaction initiates PAMP-triggered immunity (PTI), which sometimes halts infection before the virus gains a hold in the plant. However, plant viruses have evolved the means to suppress PTI by interfering with recognition at the plasma membrane. Effector-triggered immunity involves the direct or indirect recognition of the virus proteins used to subvert PTI by plant R proteins (Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response. 2006 Cell 124: 803-814). Virus virulence determinants suppress the host RNA silencing response.
Genetic engineering offers a means of incorporating new virus resistance traits into existing plant varieties. The initial attempts to create transgenes conferring virus resistance were based on the pathogen-derived resistance determinants, for example, the expression of virus coat protein genes in transgenic plants was shown to induce protective effects. Since then, a large variety of virus genes encoding structural and non-structural proteins has also been shown to confer resistance to disease (Strategies for antiviral resistance in transgenic plants. 2008 Molecular Plant Pathology 9: 73-83). Subsequently, non-coding virus RNAs have been shown to be a potential trigger for virus resistance in transgenic plants, which led to the discovery of RNA silencing.
Plants have evolved a robust innate immune system that exhibits striking similarities as well as significant differences with innate immunity in animals. For example, plants are capable of perceiving PAMPs through pattern recognition receptors that bear structural similarities to animal Toll-like receptors. In addition, plants have evolved a second surveillance system based on cytoplasmic “NB-LRR” proteins (nucleotide-binding, leucine-rich repeat) that are structurally similar to animal nucleotide-binding and oligomerization domain (NOD)-like receptors. Plant NB-LRR proteins do not detect PAMPs, but recognize proteins that viruses produce in plant cells. (Molecular diversity at the plant-pathogen interface. 2007 Dev Comp Immunol)
The number of different strategies that have been developed for creating virus and viroid resistance is one of the major success stories in biotechnology. However, few of these strategies have ever been taken past the proof of principle stage in the laboratory, or small-scale field trials. The only engineered virus-resistant plants that have been grown on a large commercial scale were transformed with complete virus transgenes, and it appears that the resistance induced is of the RNA silencing type in all these cases. That means that there is still enormous potential for overcoming the detrimental effects of plant viruses through genetic manipulation of valuable plant varieties.
With MRSA threatening to infect huge numbers of patients who make even short trips to the hospital, and the gradual increase in the number of bacteria that are resistant to all known antiobiotics, scientists are turning to new ways to conquer the killer bugs. The emergence of dangerous antibiotic resistant strains of bacteria is most prevalent in the USA where antibiotics are available over the counter and are often mishandled. The answers to these problems may be locked in the science of the former Soviet Union, and whether this potential can be unlocked depends on subtle aspects of intellectual property and patent law, since pharmaceutical companies must be able to control the revenues from a discovery:
Today’s issue of Science describes how a group of scientists led by Craig Venter have built an entire bacterial genome from scratch, i.e. starting with simple laboratory chemicals and finishing with a 582,970 base pair DNA chromosome. So is this the end of the world? Have mad scientists created a Frankenstein bug which will escape the laboratory and eat the world?
Nope.
For one thing, the molecule which has been synthesized is presently just that - an inert molecule of DNA. Not until it is inserted into a “hollow” bacterial host from which the DNA has been removed can it come “alive” and start to replicate itself and direct the activities of the cell.
But more importantly, this synthetic biology project is based on an existing organism (Mycoplasma genitalium), which has been around for a long time, so it’s not exactly new. Venter’s team has reproduced this reather than creating anything new.
Finally, some bacteria degrade explosives, others prefer boiling methanol - in other words, if it is possible, nature has already thought of it. So the article published today is nothing to lose sleep over. Of course, that doesn’t mean that at some point in the future those nasty terrorists won’t build a synthetic organism which is genuinely dangerous. But they’re not going to do it working in their garage - this is a government or large corporation-scale project which is the biological equivalent of putting a person on the moon. So if you want something to worry about, worry about climate change, your grades, or the stock market.
Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. 2008 Science Published Online January 24, 2008
We have synthesized a 582,970 bp Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted “watermarks” at intergenic sites known to tolerate transposon insertions. Overlapping “cassettes” of 5 to 7 kb, assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb (”1/8 genome”), and 144 kb (”1/4 genome”), which were all cloned as bacterial artificial chromosomes (BACs) in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination (TAR) cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.
