The 1st EMBO workshop on PVC bacteria—Planctomycetes–Verrucomicrobia–Chlamydiae superphylum: Exceptions to the bacterial definition?

The PVC superphylum is a phylogenetically supported collection of various related bacterial phyla that comprise unusual characteristics and traits. The ‘PVC’ abbreviation derives from Planctomycetes, Verrucomicrobia and Chlamydiae as members of this superphylum, while additional bacterial phyla are related. There has recently been increasing and exciting interest in the cell biology, physiology and ecology of members of this superphylum, including evolutionary implications of the complex cell organization of some species. It is timely that international researchers in the PVC superphylum field met to discuss these developments. The first meeting entirely dedicated to those bacteria, the EMBO workshop “PVC superphylum: Exceptions to the bacterial definition” was held at the Heidelberg University to catalyze the formation of a vital scientific community supporting PVC-bacterial research. More than 45 investigators from more than 20 countries (PIs, senior scientists and students) attended the meeting and produced a great starting point for future collaborative research. This Special Issue will focus on the EMBO-PVC meeting. This Perspective briefly summarizes the history of PVC-research, focusing on the key findings and provides a brief summary of the meeting with a focus on the major questions that arose during discussion and that might influence the research in the years to come.     

The bacterial replisome: back on track?

It has been postulated that bacterial DNA replication occurs via a factory mechanism in which unreplicated DNA is spooled into a centrally located replisome and newly synthesized DNA is discharged towards opposite cell poles. Although there is considerable support for this view, it does not fit with many key observations. I review new findings, and provide alternative interpretations for old findings, which challenge this model. As a whole, current data suggest that the replisome, at least in slowly growing Escherichia coli cells, tracks along a stationary chromosome. These replisomes are not stationary, tethered or restricted in their movement, but rather travel throughout the nucleoid. One possibility is that the replisome navigates along a chromosome made up of looped domains as has been previously envisioned.     

The onchocerciasis chronicle: from the beginning to the end?

The year 2012 marks the 25th anniversary of the donation of ivermectin to fight onchocerciasis and the projected date for elimination of transmission of the disease in the Americas. This review looks at the history of onchocerciasis, from its discovery through to 2025, by which time it is projected that the disease will have been eliminated as a public health problem, except in a handful of sub-Saharan countries, where it should be well on the way towards elimination.     

The α-proteobacteria: the Darwin finches of the bacterial world

The α-proteobacteria represent one of the most diverse bacterial subdivisions, displaying extreme variations in lifestyle, geographical distribution and genome size. Species for which genome data are available have been classified into a species tree based on a conserved set of vertically inherited core genes. By mapping the variation in gene content onto the species tree, genomic changes can be associated with adaptations to specific growth niches. Genes for adaptive traits are mostly located in ‘plasticity zones’ in the bacterial genome, which also contain mobile elements and are highly variable across strains. By physically separating genes for information processing from genes involved in interactions with the surrounding environment, the rate of evolutionary change can be substantially enhanced for genes underlying adaptation to new growth habitats, possibly explaining the ecological success of the α-proteo-bacterial subdivision.     

The key to development: interpreting the histone code?

Developmental stages in multicellular organisms proceed according to a temporally and spatially precise pattern of gene expression. It has become evident that changes within the chromatin structure brought about by covalent modifications of histones are of crucial importance in determining many biological processes, including development. Numerous studies have provided evidence that the enzymes responsible for the modifications of histones function in a coordinated pattern to control gene expression in the short term and, through the transferral of these modifications by inheritance to their progeny, in the long term.     

Host specificity in ectomycorrhizal communities: what do the exceptions tell us?

Classic ectomycorrhizal symbioses are mutualisms that involvethe exchange of fixed carbon for mineral nutrients between plantroots and fungi. They are unique in the way they contain featuresof both intimate and diffuse symbioses. The degree of host specificityvaries, particularly among the fungi. Here we examine two exceptionalcases of specificity to see what they tell us about the advantagesof specificity, how it is initiated, and the potential rolethat it plays in complex ecosystems. The first case involvesnon-photosynthetic epiparasitic plants, which contrary to virtuallyall other plants, exhibit high levels of specificity towardtheir fungal hosts. The second case involves suilloid fungi;this is the largest monophyletic group of ectomycorrhizal fungithat is essentially restricted to associations with a singleplant family. In both cases, new symbioses are initiated bydormant propagules that are stimulated to germinate by chemicalcues from the host. This reduces the cost of wasting propaguleson non-hosts. The advantages of specificity remain unclear inboth cases, but we argue that increased benefit to the specialistmay result from specialized physiological adaptations. We reexaminethe idea that specialist fungi may help their hosts competein complex ecosystems by reducing facultative epiparasitismby other plants, and suggest an alternative hypothesis for theobserved pattern.     

Recognition of bacterial avirulence proteins occurs inside the plant cell: a general phenomenon in resistance to bacterial diseases?

One of the recent exciting developments in the research area of plant-microbe interactions is a breakthrough in understanding part of the initial signalling between avirulent Gram-negative bacteria and resistant plants. For resistance to occur, both interacting organisms need to express matching genes, the plant resistance gene and the bacterial avirulence gene. The biochemical function of bacterial avirulence genes and the nature of the signal molecules recognized by the plant have been a mystery for a long time. Recently, several laboratories have shown that bacterial avirulence proteins function as elicitors that are perceived within the plant cell.     

The Ordovician Radiation: A Follow-up to the Cambrian Explosion?

There was a major diversification known as the Ordovician Radiation,in the period immediately following the Cambrian. This eventis unique in taxonomic, ecologic and biogeographic aspects. While all of the phyla but one were established during the Cambrianexplosion, taxonomic increases during the Ordovician were manifestat lower taxonomic levels although ordinal level diversity doubled.Marine family diversity tripled and within clade diversity increasesoccurred at the genus and species levels. The Ordovician radiationestablished the Paleozoic Evolutionary Fauna; those taxa whichdominated the marine realm for the next 250 million years. Communitystructure dramatically increased in complexity. New communitieswere established and there were fundamental shifts in dominanceand abundance. Over the past ten years, there has been an effort to examinethis radiation at different scales. In comparison with the Cambrianexplosion which appears to be more globally mediated, localand regional studies of Ordovician faunas reveal sharp transitionswith timing and magnitudes that vary geographically. These transitionssuggest a more episodic and complex history than that revealedthrough synoptic global studies alone. Despite its apparent uniqueness, we cannot exclude the possibilitythat the Ordovician radiation was an extension of Cambrian diversitydynamics. That is, the Ordovician radiation may have been anevent independent of the Cambrian radiation and thus requiringa different set of explanations, or it may have been the inevitablefollow-up to the Cambrian radiation. Future studies should focuson resolving this issue.     

CpG motifs: the active ingredient in bacterial extracts?

The use of bacteria and bacterial extracts for immunotherapy has a checkered past. Recent developments in immunology reveal that these nonspecific immune activators actually work by triggering specific receptors that are expressed by subsets of immune cells. Identification of these receptors and the molecular signaling pathways that they activate has enabled a new era of specific targeted immunotherapy using chemically synthesized mimics of pathogen molecules.     

Functional analysis of colonic bacterial metabolism: relevant to health?

With the use of molecular techniques, numerous studies have evaluated the composition of the intestinal microbiota in health and disease. However, it is of major interest to supplement this with a functional analysis of the microbiota. In this review, the different approaches that have been used to characterize microbial metabolites, yielding information on the functional end products of microbial metabolism, have been summarized. To analyze colonic microbial metabolites, the most conventional way is by application of a hypothesis-driven targeted approach, through quantification of selected metabolites from carbohydrate (e.g., short-chain fatty acids) and protein fermentation (e.g., p-cresol, phenol, ammonia, or H(2)S), secondary bile acids, or colonic enzymes. The application of stable isotope-labeled substrates can provide an elegant solution to study these metabolic pathways in vivo. On the other hand, a top-down approach can be followed by applying metabolite fingerprinting techniques based on (1)H-NMR or mass spectrometric analysis. Quantification of known metabolites and characterization of metabolite patterns in urine, breath, plasma, and fecal samples can reveal new pathways and give insight into physiological regulatory processes of the colonic microbiota. In addition, specific metabolic profiles can function as a diagnostic tool for the identification of several gastrointestinal diseases, such as ulcerative colitis and Crohn's disease. Nevertheless, future research will have to evaluate the relevance of associations between metabolites and different disease states.     

The steroid-responsive hiccup reflex arc: competitive binding to the corticosteroid-receptor?

Hiccups occurring secondary to high-doses of corticosteroids are a well-recognized problem in the field of neurosurgery. Numerous reports of oral, intravenous and intraarticular corticosteroids inducing hiccups exist in the literature. To date, there is only one case of anabolic steroids inducing hiccups. We now present a case of a patient who underwent a suboccipital craniotomy for resection of a cerebellar pontine angle meningioma. Postoperatively the patient was on high doses of Decadron and Oxandrin, an anabolic-anticatabolic agent used to combat the deleterious effects of corticosteroids. The patient suffered intractable hiccups postoperative day one, resistant to Thorazine. Oxandrin was discontinued to assess the possibility of a anabolic steroid-induced singultus. The hiccups resolved within 24 hours. This report validates the previous report on anabolic steroids inducing hiccups and exemplifies the ability for steroids as a class, due to there backbone structural homology, to induce function even as competitive inhibitors.     

The evolutionary basis of leaf senescence: method to the madness?

Recent studies on the differential expression of genes associated with leaf senescence support the long-standing interpretation of plant senescence as an organized, genetically controlled process. Sequence identities of genes that are differentially expressed in senescing leaves indicate roles in the salvage of nutrients. By considering this salvage function as the selected trait and the degeneration and death of the tissue a pleiotropic consequence of nutrient redistribution, the process of leaf senescence can be reconciled with evolutionary theories on the origins of senescence in animals.     

How close to the theoretical diffusion limit do bacterial uptake systems function?

Using a 10cm flow-through cuvette in a high precision spectrophotometer linked to a mini-computer, the growth rate dependence of Escherichia coli on glucose concentration has been studied. The specific growth rate vs bacterial mass of single cultures consuming small amounts of glucose was followed. The data were analyzed with the computer programs described previously. For neither batch nor chemostat-cultured organisms did growth follow the monod growth law. Rather, the growth rate vs residual glucose concentration has an almost abrupt change in slope, indicative of a passive diffusion barrier prior to an uptake system possessing hyperbolic dependency. Calculations showed that the diffusion through the outer membrane via the porin channels could quantitatively account for the deviations from hyperbolic dependency. Long term chemostat culture alters the bacteria so that the maximum specific growth rate is reduced, but the initial dependence on glucose concentration is increased approaching more closely the theoretical limit. Therefore there was both a change in the outer membrane channels and the uptake activity of the cytoplasmic membrane.Deceased     

Gating the bacterial mechanosensitive channels: MscS a new paradigm?

Mechanosensitive channels play major roles in protecting bacteria from hypo-osmotic shock. In the millisecond timescale they must achieve the transition from tightly closed oligomers to large, relatively non-discriminating pores. The crystal structure for MscL, combined with genetic and biochemical analysis, provided the initial insights for the mechanism by which this structural transition might be made. Discovery of the gene for a second class of mechanosensitive channel, MscS, and its subsequent crystallisation, has provided a new paradigm for mechanosensation, enabling a deeper understanding of the mechanisms of sensing membrane tension.     

Animal definition: a necessity for the validity of animal experiments?

In most scientific journals, experimental animals are described poorly. Whether this is scientifically justified is discussed in this article. It was concluded that when laboratory animals are used in scientific experiments, which almost always are of a quantitative nature, a detailed animal definition is imperative.     

The somatopause: to treat or not to treat?

There is much evidence that some aspects of ageing are similar to those observed in selective hormone deficiencies during adulthood. Replacement therapy in hypogonadism and/or growth hormone (GH) deficiency in adulthood is very successful in reversing the related clinical symptomatology. However, preliminary studies of GH treatment in the normal elderly have been largely disappointing: an increase in muscle mass is only accompanied by improved muscle strength if exercise is also increased during this period. No real benefit of GH therapy, additional to that of exercise, has been reported. Epidemiological studies indicate a relationship between high-normal insulin-like growth factor-I levels and cancer development. No definitive answers can presently be given regarding the safety of long-term GH therapy in otherwise healthy individuals during the somatopause.